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Tamborelli A, Mujica ML, Amaranto M, Barra JL, Rivas G, Godino A, Dalmasso P. L-Lactate Electrochemical Biosensor Based on an Integrated Supramolecular Architecture of Multiwalled Carbon Nanotubes Functionalized with Avidin and a Recombinant Biotinylated Lactate Oxidase. Biosensors (Basel) 2024; 14:196. [PMID: 38667189 PMCID: PMC11048174 DOI: 10.3390/bios14040196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
L-Lactate is an important bioanalyte in the food industry, biotechnology, and human healthcare. In this work, we report the development of a new L-lactate electrochemical biosensor based on the use of multiwalled carbon nanotubes non-covalently functionalized with avidin (MWCNT-Av) deposited at glassy carbon electrodes (GCEs) as anchoring sites for the bioaffinity-based immobilization of a new recombinant biotinylated lactate oxidase (bLOx) produced in Escherichia coli through in vivo biotinylation. The specific binding of MWCNT-Av to bLOx was characterized by amperometry, surface plasmon resonance (SPR), and electrochemical impedance spectroscopy (EIS). The amperometric detection of L-lactate was performed at -0.100 V, with a linear range between 100 and 700 µM, a detection limit of 33 µM, and a quantification limit of 100 µM. The proposed biosensor (GCE/MWCNT-Av/bLOx) showed a reproducibility of 6.0% and it was successfully used for determining L-lactate in food and enriched serum samples.
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Affiliation(s)
- Alejandro Tamborelli
- CIQA, CONICET, Departamento de Ingeniería Química, Facultad Regional Córdoba, Universidad Tecnológica Nacional, Maestro López esq. Cruz Roja Argentina, Córdoba 5016, Argentina;
- INFIQC, CONICET-UNC, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina;
| | - Michael López Mujica
- INFIQC, CONICET-UNC, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina;
| | - Marilla Amaranto
- CIQUIBIC, CONICET-UNC, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina; (M.A.); (J.L.B.)
| | - José Luis Barra
- CIQUIBIC, CONICET-UNC, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina; (M.A.); (J.L.B.)
| | - Gustavo Rivas
- INFIQC, CONICET-UNC, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina;
| | - Agustina Godino
- CIQUIBIC, CONICET-UNC, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina; (M.A.); (J.L.B.)
| | - Pablo Dalmasso
- CIQA, CONICET, Departamento de Ingeniería Química, Facultad Regional Córdoba, Universidad Tecnológica Nacional, Maestro López esq. Cruz Roja Argentina, Córdoba 5016, Argentina;
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Kaur C, Asrith KP, Ramachandra SG, Hegde NR. Immunoinformatics-guided recombinant polypeptide-based enzyme-linked immunosorbent assay for seromonitoring of laboratory animals for minute virus of mice and Kilham rat virus. PLoS One 2024; 19:e0298742. [PMID: 38412152 PMCID: PMC10898725 DOI: 10.1371/journal.pone.0298742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
Subclinical infection of laboratory animals with one or more of several pathogens affects the results of experiments on animals. Monitoring the health of laboratory animals encompasses routine surveillance for pathogens, including several viruses. This study aimed to explore the development of an alternative assay to the existing ones for detecting infection of mice and rats with the parvoviruses minute virus of mice (MVM) and Kilham rat virus (KRV), respectively. Full-length VP2 and NS1 proteins of these parvoviruses, besides fragments containing multiple predicted epitopes stitched together, were studied for serological detection. The optimal dilution of full-length proteins and antigenic regions containing predicted epitopes for coating, test sera, and conjugate was determined using a checkerboard titration at each step. The assays were evaluated vis-à-vis commercially available ELISA kits. The results showed that an engineered fusion of fragments containing multiple predicted MVM VP2 and NS1 epitopes was better than either of the full-length proteins for detecting antibodies in 90% of the tested sera samples. For KRV ELISA, full-length VP2 was better compared to other individual recombinant protein fragments or combinations thereof for the detection of antibodies in sera. This report is the first description of an ELISA for KRV and an improved assay for MVM. Importantly, our assays could be exploited with small volumes of sera. The results also demonstrate the utility of immunoinformatics-driven polypeptide engineering in the development of diagnostic assays and the potential to develop better tests for monitoring the health status of laboratory animals.
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Bernardotto S, Frasson I, Faravelli S, Morelli A, Schiavon E, Moscatiello GY, Violatto MB, Pinnola A, Canciani A, Mattarei A, Rossi G, Brini M, Pasetto L, Bonetto V, Bigini P, Forneris F, Richter SN, Morpurgo M. Efficient SARS-CoV-2 infection antagonization by rhACE2 ectodomain multimerized onto the Avidin-Nucleic-Acid-NanoASsembly. Biomaterials 2023; 303:122394. [PMID: 38007919 DOI: 10.1016/j.biomaterials.2023.122394] [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: 06/30/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
Nanodecoy systems based on analogues of viral cellular receptors assembled onto fluid lipid-based membranes of nano/extravescicles are potential new tools to complement classic therapeutic or preventive antiviral approaches. The need for lipid-based membranes for transmembrane receptor anchorage may pose technical challenges along industrial translation, calling for alternative geometries for receptor multimerization. Here we developed a semisynthetic self-assembling SARS-CoV-2 nanodecoy by multimerizing the biotin labelled virus cell receptor -ACE2- ectodomain onto a poly-avidin nanoparticle (NP) based on the Avidin-Nucleic-Acid-NanoASsembly-ANANAS. The ability of the assembly to prevent SARS-CoV-2 infection in human lung cells and the affinity of the ACE2:viral receptor-binding domain (RBD) interaction were measured at different ACE2:NP ratios. At ACE2:NP = 30, 90 % SARS-CoV-2 infection inhibition at ACE2 nanomolar concentration was registered on both Wuhan and Omicron variants, with ten-fold higher potency than the monomeric protein. Lower and higher ACE2 densities were less efficient suggesting that functional recognition between multi-ligand NPs and multi-receptor virus surfaces requires optimal geometrical relationships. In vivo studies in mice showed that the biodistribution and safety profiles of the nanodecoy are potentially suitable for preventing viral infection upon nasal instillation. Viral receptor multimerization using ANANAS is a convenient process which, in principle, could be rapidly adapted to counteract also other viral infections.
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Affiliation(s)
- Simone Bernardotto
- Pharmaceutical and Pharmacological Sciences Dept (DSF), University of Padova, Via Marzolo, 5. 35131, Padova, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine (DMM), University of Padova, Via A. Gabelli, 63, 35121, Padova, Italy
| | - Silvia Faravelli
- The Armenise-Harvard Laboratory of Structural Biology, Dept. Biology and Biotechnology, University of Pavia, Via Ferrata 9/A, 27100, Pavia, Italy
| | - Annalisa Morelli
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Italy, Via Mario Negri 2, 20156, Milano, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Elisa Schiavon
- Pharmaceutical and Pharmacological Sciences Dept (DSF), University of Padova, Via Marzolo, 5. 35131, Padova, Italy
| | - Giulia Yuri Moscatiello
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Italy, Via Mario Negri 2, 20156, Milano, Italy
| | - Martina Bruna Violatto
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Italy, Via Mario Negri 2, 20156, Milano, Italy
| | - Alberta Pinnola
- The Armenise-Harvard Laboratory of Structural Biology, Dept. Biology and Biotechnology, University of Pavia, Via Ferrata 9/A, 27100, Pavia, Italy
| | - Anselmo Canciani
- The Armenise-Harvard Laboratory of Structural Biology, Dept. Biology and Biotechnology, University of Pavia, Via Ferrata 9/A, 27100, Pavia, Italy
| | - Andrea Mattarei
- Pharmaceutical and Pharmacological Sciences Dept (DSF), University of Padova, Via Marzolo, 5. 35131, Padova, Italy
| | - Gianpaolo Rossi
- Department of Medicine (DIMED), University of Padova, Via Giustiniani, 2, 35131, Padova, Italy
| | - Marisa Brini
- Department of Biology (DIBIO), Viale G. Colombo, 3, 35131, Padova, Italy
| | - Laura Pasetto
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Italy, Via Mario Negri 2, 20156, Milano, Italy
| | - Valentina Bonetto
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Italy, Via Mario Negri 2, 20156, Milano, Italy
| | - Paolo Bigini
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Italy, Via Mario Negri 2, 20156, Milano, Italy
| | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Dept. Biology and Biotechnology, University of Pavia, Via Ferrata 9/A, 27100, Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine (DMM), University of Padova, Via A. Gabelli, 63, 35121, Padova, Italy; Microbiology and Virology Unit, Padua University Hospital, 35121, Padua, Italy.
| | - Margherita Morpurgo
- Pharmaceutical and Pharmacological Sciences Dept (DSF), University of Padova, Via Marzolo, 5. 35131, Padova, Italy.
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Sakaguchi A, Tanaka Y, Shoji E, Takeshima T, Sakamaki R, Matsuba T, Kurihara Y. Rapid, simple, and effective strategy to produce monoclonal antibodies targeting protein structures using hybridoma technology. J Biol Eng 2023; 17:24. [PMID: 36997993 DOI: 10.1186/s13036-023-00345-9] [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: 11/29/2022] [Accepted: 03/22/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Monoclonal antibodies are essential in life science research and developing antibody drugs and test drugs. Various methods have been developed to obtain monoclonal antibodies, among which hybridoma technology continues to be widely used. However, developing a rapid and efficient method for obtaining conformation-specific antibodies using hybridoma technology remains challenging. We previously developed the membrane-type immunoglobulin-directed hybridoma screening (MIHS) method, which is a flow cytometry-based screening technique based on the interaction between the B-cell receptor expressed on the hybridoma cell surface and the antigen protein, to obtain conformation-specific antibodies. RESULTS In this study, we proposed a streptavidin-anchored ELISA screening technology (SAST) as a secondary screening method that retains the advantages of the MIHS method. Anti-enhanced green fluorescent protein monoclonal antibodies were generated as a model experiment, and their structural recognition abilities were examined. Examination of the reaction profiles showed that all monoclonal antibodies obtained in this study recognize the conformational epitopes of the protein antigen. Furthermore, these monoclonal antibodies were classified into two groups: those with binding activities against partially denatured proteins and those with complete loss of binding activities. Next, when screening monoclonal antibodies by the MIHS method as the first screening, we found that monoclonal antibodies with stronger binding constants may be selected by double-staining for hybridomas with fluorescently labeled target antigens and fluorescently labeled B cell receptor antibodies. CONCLUSIONS The proposed two-step screening method, which incorporates MIHS and SAST, constitutes a rapid, simple, and effective strategy to obtain conformation-specific monoclonal antibodies generated through hybridoma technology. The novel monoclonal antibody screening strategy reported herein could accelerate the development of antibody drugs and antibody tests.
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Affiliation(s)
- Atsumi Sakaguchi
- Laboratory of Molecular Biology, Faculty of Engineering, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama, Kanagawa, 240-8501, Japan
- Biomaterials Analysis Division, Open Facility Center, Tokyo Institute of Technology, Midori, Yokohama, Kanagawa, Japan
| | - Yoichiro Tanaka
- Instrumental Analysis Center, Yokohama National University, Hodogaya, Yokohama, Kanagawa, Japan
| | - Eiki Shoji
- Laboratory of Molecular Biology, Faculty of Engineering, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama, Kanagawa, 240-8501, Japan
| | - Teppei Takeshima
- Department of Urology and Renal Transplantation, Yokohama City University Medical Center, Yokohama, Japan
| | - Rina Sakamaki
- Bioscience Division, Tosoh Corporation, Ebina, Kanagawa, Japan
| | - Takao Matsuba
- Bioscience Division, Tosoh Corporation, Ebina, Kanagawa, Japan
| | - Yasuyuki Kurihara
- Laboratory of Molecular Biology, Faculty of Engineering, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama, Kanagawa, 240-8501, Japan.
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Du M, Hou Z, Liu L, Xuan Y, Chen X, Fan L, Li Z, Xu B. 1Progress, applications, challenges and prospects of protein purification technology. Front Bioeng Biotechnol 2022; 10:1028691. [PMID: 36561042 PMCID: PMC9763899 DOI: 10.3389/fbioe.2022.1028691] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 08/26/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Protein is one of the most important biological macromolecules in life, which plays a vital role in cell growth, development, movement, heredity, reproduction and other life activities. High quality isolation and purification is an essential step in the study of the structure and function of target proteins. Therefore, the development of protein purification technologies has great theoretical and practical significance in exploring the laws of life activities and guiding production practice. Up to now, there is no forthcoming method to extract any proteins from a complex system, and the field of protein purification still faces significant opportunities and challenges. Conventional protein purification generally includes three steps: pretreatment, rough fractionation, and fine fractionation. Each of the steps will significantly affect the purity, yield and the activity of target proteins. The present review focuses on the principle and process of protein purification, recent advances, and the applications of these technologies in the life and health industry as well as their far-reaching impact, so as to promote the research of protein structure and function, drug development and precision medicine, and bring new insights to researchers in related fields.
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Affiliation(s)
- Miao Du
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Zhuru Hou
- Science and Technology Centre, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China,Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China,*Correspondence: Ling Liu, ; Benjin Xu,
| | - Yan Xuan
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Xiaocong Chen
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Lei Fan
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Zhuoxi Li
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China,Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China,*Correspondence: Ling Liu, ; Benjin Xu,
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Mohsin AZ, Sukor R, Selamat J, Meor Hussin AS, Ismail IH, Azri FA, Mustafa RR, Mansor M. Development of biotin-streptavidin amplified peptide antibody-based ELISA for quantification of αS1-casein in goat milk. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Koh CY, Shih N, Yip CYC, Li AWL, Chen W, Amran FS, Leong EJE, Iyer JK, Croft G, Mazlan MIB, Chee YL, Yap ES, Monroe DM, Hoffman M, Becker RC, de Kleijn DPV, Verma V, Gupta A, Chaudhary VK, Richards AM, Kini RM, Chan MY. Efficacy and safety of next-generation tick transcriptome-derived direct thrombin inhibitors. Nat Commun 2021; 12:6912. [PMID: 34824278 PMCID: PMC8617063 DOI: 10.1038/s41467-021-27275-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/28/2021] [Indexed: 01/18/2023] Open
Abstract
Despite their limitations, unfractionated heparin (UFH) and bivalirudin remain standard-of-care parenteral anticoagulants for percutaneous coronary intervention (PCI). We discovered novel direct thrombin inhibitors (DTIs) from tick salivary transcriptomes and optimised their pharmacologic activity. The most potent, ultravariegin, inhibits thrombin with a Ki of 4.0 pM, 445-fold better than bivalirudin. Unexpectedly, despite their greater antithrombotic effect, variegin/ultravariegin demonstrated less bleeding, achieving a 3-to-7-fold wider therapeutic index in rodent thrombosis and bleeding models. When used in combination with aspirin and ticagrelor in a porcine model, variegin/ultravariegin reduced stent thrombosis compared with antiplatelet therapy alone but achieved a 5-to-7-fold lower bleeding time than UFH/bivalirudin. Moreover, two antibodies screened from a naïve human antibody library effectively reversed the anticoagulant activity of ultravariegin, demonstrating proof-of-principle for antidote reversal. Variegin and ultravariegin are promising translational candidates for next-generation DTIs that may reduce peri-PCI bleeding in the presence of antiplatelet therapy.
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Affiliation(s)
- Cho Yeow Koh
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Norrapat Shih
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christina Y. C. Yip
- grid.412106.00000 0004 0621 9599Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Aaron Wei Liang Li
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Weiming Chen
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fathiah S. Amran
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Esther Jia En Leong
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Janaki Krishnamoorthy Iyer
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Grace Croft
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Muhammad Ibrahim Bin Mazlan
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yen-Lin Chee
- Department of Haematology, National Cancer Institute, Singapore, Singapore
| | - Eng-Soo Yap
- Department of Haematology, National Cancer Institute, Singapore, Singapore
| | - Dougald M. Monroe
- grid.10698.360000000122483208Division of Hematology/Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Maureane Hoffman
- grid.26009.3d0000 0004 1936 7961Department of Pathology, Duke University, Durham, NC USA
| | - Richard C. Becker
- grid.24827.3b0000 0001 2179 9593University of Cincinnati, Cincinnati, OH USA
| | - Dominique P. V. de Kleijn
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore ,grid.7692.a0000000090126352Department of Vascular Surgery, University Medical Center Utrecht & Netherlands heart Institute, Utrecht, The Netherlands
| | - Vaishali Verma
- grid.8195.50000 0001 2109 4999Centre for Innovation in Infectious Disease Research, Education, and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Amita Gupta
- grid.8195.50000 0001 2109 4999Centre for Innovation in Infectious Disease Research, Education, and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Vijay K. Chaudhary
- grid.8195.50000 0001 2109 4999Centre for Innovation in Infectious Disease Research, Education, and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - A. Mark Richards
- grid.410759.e0000 0004 0451 6143Cardiovascular Research Institute, NUHS, Singapore, Singapore ,grid.29980.3a0000 0004 1936 7830Christchurch Heart Institute, University of Otago, Otago, New Zealand
| | - R. Manjunatha Kini
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Pharmacology, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mark Y. Chan
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore ,grid.488497.e0000 0004 1799 3088Cardiac Department, National University Heart Centre, Singapore, Singapore
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Agarwal G, Gabrani R. Identification of Peptide Binders to Truncated Recombinant Chikungunya Virus Envelope Protein 2 Using Phage Display Technology and Their In Silico Characterization. Protein Pept Lett 2021; 28:508-519. [PMID: 33121397 DOI: 10.2174/0929866527666201029144245] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/08/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
AIM To identify and characterize peptide binders to truncated recombinant chikungunya virus envelope protein 2. BACKGROUND Despite extensive research on the chikungunya virus (CHIKV), the specific antiviral treatment's unavailability has stressed the need for the urgent development of therapeutics. The Envelope protein 2 (E2) of CHIKV that displays putative receptor binding sites and specific epitopes for virus neutralizing antibodies is a critical target for the therapeutic intervention. OBJECTIVE The study aims to identify the unique peptides that can bind to truncated E2 protein of CHIKV and further explore their properties as potential therapeutic candidate. METHODS A stretch of CHIKV-E2 (rE2), which is prominently exposed on the surface of virion, was used as bait protein to identify peptide binders to the CHIKV-rE2 using a 12-mer phage display peptide library. Three rounds of biopanning yielded several peptide binders to CHIKV-rE2 and their binding affinities were compared by phage ELISA. Additionally, a fully flexible-blind docking simulation investigated the possible binding modes of the selected peptides. Furthermore, the selected peptides were characterized and their ADMET properties were explored in silico. RESULTS Five peptides were identified as potential binders based on their robust reactivity to the bait protein. The selected peptides appeared to interact with the crucial residues that were notably exposed on the surface of E1-E2 trimeric structure. The explored in silico studies suggested their non-allergenicity, non-toxicity and likeliness to be antiviral. CONCLUSION The potential binding peptides of CHIKV-rE2 protein were identified using phage display technology and characterized in silico. The selected peptides could be further used for the development of therapeutics against the CHIKV infection.>.
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Affiliation(s)
- Garima Agarwal
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP 201309, India
| | - Reema Gabrani
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP 201309, India
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Verma V, Joshi G, Gupta A, Chaudhary VK. An efficient ORF selection system for DNA fragment libraries based on split beta-lactamase complementation. PLoS One 2020; 15:e0235853. [PMID: 32701967 PMCID: PMC7377443 DOI: 10.1371/journal.pone.0235853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/23/2020] [Indexed: 11/29/2022] Open
Abstract
PCR-based amplification of annotated genes has allowed construction of expression clones at genome-scale using classical and recombination-based cloning technologies. However, genome-scale expression and purification of proteins for down-stream applications is often limited by challenges such as poor expression, low solubility, large size of multi-domain proteins, etc. Alternatively, DNA fragment libraries in expression vectors can serve as the source of protein fragments with each fragment encompassing a function of its whole protein counterpart. However, the random DNA fragmentation and cloning result in only 1 out of 18 clones being in the correct open-reading frame (ORF), thus, reducing the overall efficiency of the system. This necessitates the selection of correct ORF before expressing the protein fragments. This paper describes a highly efficient ORF selection system for DNA fragment libraries, which is based on split beta-lactamase protein fragment complementation. The system has been designed to allow seamless transfer of selected DNA fragment libraries into any downstream vector systems using a restriction enzyme-free cloning strategy. The strategy has been applied for the selection of ORF using model constructs to show near 100% selection of the clone encoding correct ORF. The system has been further validated by construction of an ORF-selected DNA fragment library of 30 genes of M. tuberculosis. Further, we have successfully demonstrated the cytosolic expression of ORF-selected protein fragments in E. coli.
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Affiliation(s)
- Vaishali Verma
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Gopal Joshi
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Amita Gupta
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Vijay K. Chaudhary
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail:
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Lomakin YA, Kaminskaya AN, Stepanov AV, Shmidt AA, Gabibov AG, Belogurov AA. Probing Surface Membrane Receptors Using Engineered Bacteriophage Bioconjugates. Bioconjug Chem 2019; 30:1500-1506. [PMID: 31021608 DOI: 10.1021/acs.bioconjchem.9b00218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Specific recognition of ligands by surface receptors of eukaryotic cells is a fundamental process in sensing of the exogenous environment, including cell-to-cell communication. These interactions are therefore widely probed in both basic studies and drug development to enhance or interrupt them. Here, we designed a high-throughput publicly available platform for visualization and selection of eukaryotic cells according to the specificity of surface-exposed receptors by consolidation of phage display and flow cytometry techniques. Polypeptide ligands for membrane receptors are incorporated into every copy of p3 protein of M13K07 bacteriophage, which is intracellularly biotinylated to further accept PE-Cy7-labled streptavidin. Transgenic antigen-specific B-cells expressing membrane-tethered lymphoid B-cell receptor in a single-chain format interacted with engineered bacteriophages exposing the polypeptide ligand with an unprecedented selectivity of 97% and a false-positive detection value of 2.0%. Multivalent binding of the phage bioconjugates with the receptor provided significantly better specificity and sensitivity allowing application of engineered bacteriophage bioconjugates at a concentration 3 orders of magnitude lower in comparison with synthetic biotinylated peptide. We suggest that the platform described in this work may be applied either for routine staining or characterization of orphan membrane receptors exposed on the surface of living mammalian cells in their native environment.
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Affiliation(s)
- Yakov A Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , Moscow , Russia , 117997.,Institute of Fundamental Medicine and Biology , Kazan Federal University , Kazan , Russia , 420012
| | - Alena N Kaminskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , Moscow , Russia , 117997
| | - Alexey V Stepanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , Moscow , Russia , 117997.,Institute of Fundamental Medicine and Biology , Kazan Federal University , Kazan , Russia , 420012
| | - Anna A Shmidt
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , Moscow , Russia , 117997
| | - Alexander G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , Moscow , Russia , 117997.,Lomonosov Moscow State University , Moscow , Russia , 119991
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , Moscow , Russia , 117997.,Lomonosov Moscow State University , Moscow , Russia , 119991
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