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Sheikhi A, Baghaie L, Rahbarizadeh F, Safarzadeh Kozani P, Moradian C, Davidi M, Baharifar N, Kaboli G, Sheikhi M, Li Y, Meghdadi M, Yaish AM, Yu AH, Harless WW, Szewczuk MR. Novel sACE2-Anti-CD16VHH Fusion Protein Surreptitiously Inhibits SARS-CoV-2 Variant Spike Proteins and Macrophage Cytokines, and Activates Natural Killer Cell Cytotoxicity. Vaccines (Basel) 2025; 13:199. [PMID: 40006745 PMCID: PMC11860277 DOI: 10.3390/vaccines13020199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 01/28/2025] [Accepted: 02/10/2025] [Indexed: 02/27/2025] Open
Abstract
Background/Objectives: The SARS-CoV-2's high mutations and replication rates contribute to its high infectivity and resistance to current vaccinations and treatments. The primary cause of resistance to most current treatments aligns within the coding regions for the spike S protein of SARS-CoV-2 that has mutated. As a potential novel immunotherapy, we generated a novel fusion protein composed of a soluble ACE2 (sACE2) linked to llama-derived anti-CD16 that targets different variants of spike proteins and enhances natural killer cells to target infected cells. Methods: Here, we generated a novel sACE2-AntiCD16VHH fusion protein using a Gly4Ser linker, synthesized and cloned into the pLVX-EF1alpha-IRES-Puro vector, and further expressed in ExpiCHO-S cells and purified using Ni+NTA chromatography. Results: The fusion protein significantly blocked SARS-CoV-2 alpha, beta, delta, gamma, and omicron S-proteins binding and activating angiotensin-converting enzyme receptor-2 (ACE2) on ACE2-expressing RAW-Blue macrophage cells and the secretion of several key inflammatory cytokines, G-CSF, MIP-1A, and MCP-1, implicated in the cytokine release storm (CRS). The sACE2-Anti-CD16VHH fusion protein also bridged NK cells to ACE2-expressing human lung carcinoma A549 cells and significantly activated NK-dependent cytotoxicity. Conclusions: The findings show that a VHH directed against CD16 could be an excellent candidate to be linked to soluble ACE2 to generate a bi-specific molecule (sACE2-AntiCD16VHH) suitable for bridging effector cells and infected target cells to inhibit SARS-CoV-2 variant spike proteins binding to the ACE2 receptor in the RAW-Blue cell line and pro-inflammatory cytokines and to activate natural killer cell cytotoxicity.
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Affiliation(s)
- Abdolkarim Sheikhi
- Department of Biomedical & Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada;
- Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful 64616-43993, Iran; (N.B.); (G.K.)
| | - Leili Baghaie
- Department of Biomedical & Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada;
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran; (F.R.); (P.S.K.); (C.M.)
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran 14115-331, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran; (F.R.); (P.S.K.); (C.M.)
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran 14115-331, Iran
| | - Cobra Moradian
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran; (F.R.); (P.S.K.); (C.M.)
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran 14115-331, Iran
| | - Mohammadreza Davidi
- Faculty of Medicine, Kazeroon Azad University, Kazeroon 14778-93855, Iran; (M.D.); (M.S.)
| | - Narges Baharifar
- Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful 64616-43993, Iran; (N.B.); (G.K.)
| | - Golnaz Kaboli
- Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful 64616-43993, Iran; (N.B.); (G.K.)
| | - Mehdi Sheikhi
- Faculty of Medicine, Kazeroon Azad University, Kazeroon 14778-93855, Iran; (M.D.); (M.S.)
| | - Yunfan Li
- Faculty of Arts and Science, Queen’s University, Kingston, ON K7L 3N9, Canada;
| | - Mohammadamin Meghdadi
- Faculty of Health Sciences, Queen’s University, Kingston, ON K7L 3N9, Canada; (M.M.); (A.M.Y.); (A.H.Y.)
| | - Abdulrahman M. Yaish
- Faculty of Health Sciences, Queen’s University, Kingston, ON K7L 3N9, Canada; (M.M.); (A.M.Y.); (A.H.Y.)
| | - Aiden H. Yu
- Faculty of Health Sciences, Queen’s University, Kingston, ON K7L 3N9, Canada; (M.M.); (A.M.Y.); (A.H.Y.)
| | | | - Myron R. Szewczuk
- Department of Biomedical & Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada;
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2
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Zhang BW, Fajer M, Chen W, Moraca F, Wang L. Leveraging the Thermodynamics of Protein Conformations in Drug Discovery. J Chem Inf Model 2025; 65:252-264. [PMID: 39681511 DOI: 10.1021/acs.jcim.4c01612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
Abstract
As the name implies, structure-based drug design requires confidence in the holo complex structure. The ability to clarify which protein conformation to use when ambiguity arises would be incredibly useful. We present a large scale validation of the computational method Protein Reorganization Free Energy Perturbation (PReorg-FEP) and demonstrate its quantitative accuracy in selecting the correct protein conformation among candidate models in apo or ligand induced states for 14 different systems. These candidate conformations are pulled from various drug discovery related campaigns: cryptic conformations induced by novel hits in lead identification, binding site rearrangement during lead optimization, and conflicting structural biology models. We also show an example of a pH-dependent conformational change, relevant to protein design.
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Affiliation(s)
- Bin W Zhang
- Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States
| | - Mikolai Fajer
- Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States
| | - Wei Chen
- Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States
| | - Francesca Moraca
- Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States
| | - Lingle Wang
- Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States
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3
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Jha R, Kinna A, Hotblack A, Bughda R, Bulek A, Gannon I, Ilca T, Allen C, Lamb K, Dolor A, Scott I, Parekh F, Sillibourne J, Cordoba S, Onuoha S, Thomas S, Ferrari M, Pule M. Designer Small-Molecule Control System Based on Minocycline-Induced Disruption of Protein-Protein Interaction. ACS Chem Biol 2024; 19:308-324. [PMID: 38243811 PMCID: PMC10877577 DOI: 10.1021/acschembio.3c00521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/01/2024] [Accepted: 01/04/2024] [Indexed: 01/22/2024]
Abstract
A versatile, safe, and effective small-molecule control system is highly desirable for clinical cell therapy applications. Therefore, we developed a two-component small-molecule control system based on the disruption of protein-protein interactions using minocycline, an FDA-approved antibiotic with wide availability, excellent biodistribution, and low toxicity. The system comprises an anti-minocycline single-domain antibody (sdAb) and a minocycline-displaceable cyclic peptide. Here, we show how this versatile system can be applied to OFF-switch split CAR systems (MinoCAR) and universal CAR adaptors (MinoUniCAR) with reversible, transient, and dose-dependent suppression; to a tunable T cell activation module based on MyD88/CD40 signaling; to a controllable cellular payload secretion system based on IL12 KDEL retention; and as a cell/cell inducible junction. This work represents an important step forward in the development of a remote-controlled system to precisely control the timing, intensity, and safety of therapeutic interventions.
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Affiliation(s)
- Ram Jha
- Autolus
Therapeutics, London W12 7FP, U.K.
- Research
Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, U.K.
| | | | - Alastair Hotblack
- Research
Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, U.K.
| | | | - Anna Bulek
- Autolus
Therapeutics, London W12 7FP, U.K.
| | | | - Tudor Ilca
- Autolus
Therapeutics, London W12 7FP, U.K.
| | | | | | | | - Ian Scott
- Autolus
Therapeutics, London W12 7FP, U.K.
| | | | | | | | | | | | | | - Martin Pule
- Autolus
Therapeutics, London W12 7FP, U.K.
- Research
Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, U.K.
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4
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Nguyen TD, Bordeau BM, Balthasar JP. Use of Payload Binding Selectivity Enhancers to Improve Therapeutic Index of Maytansinoid-Antibody-Drug Conjugates. Mol Cancer Ther 2023; 22:1332-1342. [PMID: 37493255 PMCID: PMC10811745 DOI: 10.1158/1535-7163.mct-22-0804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/03/2023] [Accepted: 07/21/2023] [Indexed: 07/27/2023]
Abstract
Systemic exposure to released cytotoxic payload contributes to the dose-limiting off-target toxicities of anticancer antibody-drug conjugates (ADC). In this work, we present an "inverse targeting" strategy to optimize the therapeutic selectivity of maytansinoid-conjugated ADCs. Several anti-maytansinoid sdAbs were generated via phage-display technology with binding IC50 values between 10 and 60 nmol/L. Co-incubation of DM4 with the anti-maytansinoid sdAbs shifted the IC50 value of DM4 up to 250-fold. Tolerability and efficacy of 7E7-DM4 ADC, an anti-CD123 DM4-conjugated ADC, were assessed in healthy and in tumor-bearing mice, with and without co-administration of an anti-DM4 sdAb. Co-administration with anti-DM4 sdAb reduced 7E7-DM4-induced weight loss, where the mean values of percentage weight loss at nadir for mice receiving ADC+saline and ADC+sdAb were 7.9% ± 3% and 3.8% ± 1.3% (P < 0.05). In tumor-bearing mice, co-administration of the anti-maytansinoid sdAb did not negatively affect the efficacy of 7E7-DM4 on tumor growth or survival following dosing of the ADC at 1 mg/kg (P = 0.49) or at 10 mg/kg (P = 0.9). Administration of 7E7-DM4 at 100 mg/kg led to dramatic weight loss, with 80% of treated mice succumbing to toxicity before the appearance of mortality relating to tumor growth in control mice. However, all mice receiving co-dosing of 100 mg/kg 7E7-DM4 with anti-DM4 sdAb were able to tolerate the treatment, which enabled reduction in tumor volume to undetectable levels and to dramatic improvements in survival. In summary, we have demonstrated the utility and feasibility of the application of anti-payload antibody fragments for inverse targeting to improve the selectivity and efficacy of anticancer ADC therapy.
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Affiliation(s)
- Toan D. Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214
| | - Brandon M. Bordeau
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214
| | - Joseph P. Balthasar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214
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5
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Yang H, Qi M, He Q, Hwang SH, Yang J, McCoy M, Morisseau C, Zhao S, Hammock BD. Quantification of soluble epoxide hydrolase inhibitors in experimental and clinical samples using the nanobody-based ELISA. J Pharm Anal 2023; 13:1013-1023. [PMID: 37842656 PMCID: PMC10568103 DOI: 10.1016/j.jpha.2023.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 10/17/2023] Open
Abstract
To ensure proper dosage of a drug, analytical quantification of it in biofluid is necessary. Liquid chromatography mass spectrometry (LC-MS) is the conventional method of choice as it permits accurate identification and quantification. However, it requires expensive instrumentation and is not appropriate for bedside use. Using soluble epoxide hydrolase (sEH) inhibitors (EC5026 and TPPU) as examples, we report development of a nanobody-based enzyme-linked immunosorbent assay (ELISA) for such small molecules and its use to accurately quantify the drug chemicals in human samples. Under optimized conditions, two nanobody-based ELISAs were successfully established for EC5026 and TPPU with low limits of detection of 0.085 ng/mL and 0.31 ng/mL, respectively, and two order of magnitude linear ranges with high precision and accuracy. The assay was designed to detect parent and two biologically active metabolites in the investigation of a new drug candidate EC5026. In addition, the ELISAs displayed excellent correlation with LC-MS analysis and evaluation of inhibitory potency. The results indicate that nanobody-based ELISA methods can efficiently analyze drug like compounds. These methods could be easily implemented by the bedside, in the field in remote areas or in veterinary practice. This work illustrates that nanobody based assays offer alternative and supplementary analytical tools to mass spectrometry for monitoring small molecule medicines during clinical development and therapy. Attributes of nanobody based pharmaceutical assays are discussed.
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Affiliation(s)
- Huiyi Yang
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Meng Qi
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
- Langfang Normal University, Langfang, Hebei, 065000, China
| | - Qiyi He
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Sung Hee Hwang
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Jun Yang
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Mark McCoy
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Suqing Zhao
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Bruce D. Hammock
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
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6
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Guo Y, Ouyang Z, He W, Zhang J, Qin Q, Jiao M, Muyldermans S, Zheng F, Wen Y. Screening and epitope characterization of diagnostic nanobody against total and activated Bacteroides fragilis toxin. Front Immunol 2023; 14:1065274. [PMID: 36845160 PMCID: PMC9950733 DOI: 10.3389/fimmu.2023.1065274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 02/12/2023] Open
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) can rapidly secrete an enterotoxin termed B. fragilis toxin (BFT), which is thought to be the only recognized virulence factor in ETBF. ETBF can cause acute diarrhea, inflammatory bowel disease (IBD), colorectal cancer, and breast cancer. BFT is divided into three subtypes, BFT1, BFT2, and BFT3. BFT1 is the most widely distributed in human B. fragilis isolates. BFT can be used as a biomarker for predicting the inflammation-cancer transformation of intestine and breast. Nanobodies have the advantages of small structure, complete antigen recognition capacity, rapid selection via phage display technology, and can be massively produced in microbial expression systems. Nanobodies have become a powerful tool for medical diagnosis and treatment. This study focuses on screening and structural characterization of nanobodies targeting full length and active BFT. By constructing prokaryotic expression systems to obtain recombinant BFT1 protein, high purity BFT1 protein was used to immunize alpacas. Phage display technology was used to construct a phage display library. The positive clones were selected by bio-panning, and the isothermal titration calorimetry was used to select high-affinity nanobodies. Then the three-dimensional structures of BFT1:Nb2.82 and BFT1:Nb3.27 were solved by crystal X-ray diffraction. We got two kinds of nanobodies, Nb2.82 targeting the BFT1 prodomain and Nb3.27 recognizing the BFT1 catalytic domain. This study provides a new strategy for the early diagnosis of ETBF and the possibility for BFT as a biomarker for diagnosing diseases.
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Affiliation(s)
- Yucheng Guo
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Zhenlin Ouyang
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Wenbo He
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Jiaxin Zhang
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Qian Qin
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Min Jiao
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fang Zheng
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China,*Correspondence: Yurong Wen, ; Fang Zheng,
| | - Yurong Wen
- Center for Microbiome Research of Med-X Institute, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China,*Correspondence: Yurong Wen, ; Fang Zheng,
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Smith CA, Sonneson GJ, Hoey RJ, Hinerman JM, Sheehy K, Walter R, Herr AB, Horn JR. Molecular recognition requires dimerization of a VHH antibody. MAbs 2023; 15:2215363. [PMID: 37243579 PMCID: PMC10228392 DOI: 10.1080/19420862.2023.2215363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023] Open
Abstract
Camelid heavy-chain-only antibodies are a unique class of antibody that possesses only a single variable domain (termed VHH) for antigen recognition. Despite their apparent canonical mechanism of target recognition, where a single VHH domain binds a single target, an anti-caffeine VHH has been observed to possess 2:1 stoichiometry. Here, the structure of the anti-caffeine VHH/caffeine complex enabled the generation and biophysical analysis of variants that were used to better understand the role of VHH homodimerization in caffeine recognition. VHH interface mutants and caffeine analogs, which were examined to probe the mechanism of caffeine binding, suggested caffeine recognition is only possible with the VHH dimer species. Correspondingly, in the absence of caffeine, the anti-caffeine VHH was found to form a dimer with a dimerization constant comparable to that observed with VH:VL domains in conventional antibody systems, which was most stable near physiological temperature. While the VHH:VHH dimer structure (at 1.13 Å resolution) is reminiscent of conventional VH:VL heterodimers, the homodimeric VHH possesses a smaller angle of domain interaction, as well as a larger amount of apolar surface area burial. To test the general hypothesis that the short complementarity-determining region-3 (CDR3) may help drive VHH:VHH homodimerization, an anti-picloram VHH domain containing a short CDR3 was generated and characterized, which revealed it also existed as dimer species in solution. These results suggest homodimer-driven recognition may represent a more common method of VHH ligand recognition, opening opportunities for novel VHH homodimer affinity reagents and helping to guide their use in chemically induced dimerization applications.
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Affiliation(s)
- Christopher A. Smith
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Gregory J. Sonneson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Robert J. Hoey
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Jennifer M. Hinerman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Kimberly Sheehy
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Richard Walter
- Shamrock Structures, LLC, Woodridge, IL, USA
- Joliet XTALPAC LLC, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - James R. Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
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Li B, Qin X, Mi LZ. Nanobodies: from structure to applications in non-injectable and bispecific biotherapeutic development. NANOSCALE 2022; 14:7110-7122. [PMID: 35535618 DOI: 10.1039/d2nr00306f] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The increasing demand for convenient, miniaturized and multifunctional antibodies necessitates the development of novel antigen-recognition molecules for biological and medical studies. Nanobodies, the functional variable regions of camelid heavy-chain-only antibodies, as a new tool, complement the conventional antibodies and are in the stage of rapid development. The outstanding advantages of nanobodies include a stable structure, easy production, excellent water solubility, high affinity toward antigens and low immunogenicity. With promising application potential, nanobodies are now increasingly applied to various studies, including protein structure analysis, microscopic imaging, medical diagnosis, and drug development. The approval of the first nanobody drug Caplacizumab by the FDA disclosed the therapeutic potential of nanobodies. The outbreak of COVID-19 accelerated the development of nanobody drugs in non-injectable and bispecific biotherapeutic applications. Herein, we reviewed recent studies on the nanobody structure, screening and their applications in protein structure analysis and nanobody drugs, especially on non-injectable nanobody and bispecific nanobody development.
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Affiliation(s)
- Bingxuan Li
- School of Life Sciences, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
| | - Xiaohong Qin
- School of Life Sciences, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
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9
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Shirshahi V, Liu G. Enhancing the analytical performance of paper lateral flow assays: From chemistry to engineering. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116200] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Karami E, Sabatier JM, Behdani M, Irani S, Kazemi-Lomedasht F. A nanobody-derived mimotope against VEGF inhibits cancer angiogenesis. J Enzyme Inhib Med Chem 2021; 35:1233-1239. [PMID: 32441172 PMCID: PMC7717616 DOI: 10.1080/14756366.2020.1758690] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vascular Endothelial Growth Factor (VEGF) promotes angiogenesis in tumours of various cancers. Monoclonal antibodies and nanobodies are one of the potent agents in the treatment of cancer. Due to their high costs, researchers are considering to design and produce peptides as a substitute approach in recent years. The aim of the current study was designing a mimotope against VEGF and evaluate its effects on cell proliferation and tube formation in the HUVEC cell line. For this, a peptide was designed against VEGF and chemically produced. The effects of synthetic peptide and nanobody on the inhibition of proliferation of HUVEC cells were examined using MTT and tube formation assays. The data indicate that the peptide was able to significantly inhibit both HUVEC cell proliferation and tube formation through inhibition of VEGF, highlighting the potential of peptides as a ‘novel’ class of candidate drugs to inhibit angiogenesis.
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Affiliation(s)
- Elmira Karami
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Jean-Marc Sabatier
- Aix-Marseille Université, Institut de Neurophysiopathologie (INP) UMR 7051, 27 boulevard Jean Moulin, Faculté de Médecine, 13385 - Marseille Cédex 5, France
| | - Mahdi Behdani
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Kazemi-Lomedasht
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Mir MA, Mehraj U, Sheikh BA, Hamdani SS. Nanobodies: The "Magic Bullets" in therapeutics, drug delivery and diagnostics. Hum Antibodies 2020; 28:29-51. [PMID: 31322555 DOI: 10.3233/hab-190390] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibodies represent a well-established class of clinical diagnostics for medical applications as well as essential research and biotechnological tools. Although both polyclonal and monoclonal antibodies are indispensable reagents in basic research and diagnostics but both of them have their limitations. Hence, there is urgent need to develop strategies aimed at production of alternative scaffolds and recombinant antibodies of smaller dimensions that could be easily produced, selected and manipulated. Unlike conventional antibodies, members of Camelidae and sharks produce antibodies composed only of heavy chains with small size, high solubility, thermal stability, refolding capacity and good tissue penetration in vivo. The discovery of these naturally occurring antibodies having only heavy-chain in Camelidae family and their further development into small recombinant nanobodies represents an attractive alternative in drug delivery, diagnostics and imaging. Nanobody derivatives are soluble, stable, versatile, have unique refolding capacities, reduced aggregation tendencies and high-target binding capabilities. They can be genetically customized to target enzymes, transmembrane proteins or molecular interactions. Their ability to recognize recessed antigenic sites has been attributed to their smaller size and the ability of the extended CDR3 loop to quickly penetrate into such epitopes. With the advent of molecular engineering and phage display technology, they can be of potential use in molecular imaging, drug delivery and therapeutics for several major diseases. In this review we present the recent advances in nanobodies for modulating immune functions, for targeting cancers, viruses, toxins and microbes as well as their utility as diagnostic and biosensor tools.
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12
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Sheikhi A, Hojjat-Farsangi M. An immunotherapeutic method for COVID-19 patients: a soluble ACE2-Anti-CD16 VHH to block SARS-CoV-2 Spike protein. Hum Vaccin Immunother 2020; 17:92-97. [PMID: 32663051 DOI: 10.1080/21645515.2020.1787066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The third outbreak of coronavirus (CoV) infection (after SARS-CoV and MERS-CoV) caused by a novel CoV (SARS-CoV-2) of the genus Beta-coronavirus has become a global pandemic. CoVs are enveloped viruses whose proteins include spike (S), membrane (M), and envelope (E) which are embedded in the viral envelope. The glycosylated S protein, which forms homo-trimeric spikes on the surface of the viral particle, mediates viral entry into host cells. SARS-CoV-2, like SARS-CoV, uses the Angiotensin-Converting Enzyme 2 (ACE2) cell surface protein for cellular entry. An attractive anti-viral approach is targeting virus entry into cells, for which three strategies are suggested: 1) direct targeting of the viral glycoprotein; 2) targeting the viral receptor on the cell surface; and 3) using soluble (s) ACE2 that binds to S protein thereby neutralizing the virus. In this article, the advantages and disadvantages of these strategies are explained. Moreover, we propose that fusion of the sACE2 to anti-CD16 to produce a bi-specific molecule could be a promising anti-viral strategy.
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Affiliation(s)
- Abdolkarim Sheikhi
- Department of Immunology, School of Medicine, Dezful University of Medical Sciences , Dezful, Iran
| | - Mohammad Hojjat-Farsangi
- Department of Oncology-Pathology, Karolinska Institute , Stockholm, Sweden.,The Persian Gulf Marine Biotechnology Medicine Research Center, Bushehr University of Medical Sciences , Bushehr, Iran
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13
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Albumin nanoparticles as nanocarriers for drug delivery: Focusing on antibody and nanobody delivery and albumin-based drugs. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2019.101471] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Hoey RJ, Eom H, Horn JR. Structure and development of single domain antibodies as modules for therapeutics and diagnostics. Exp Biol Med (Maywood) 2019; 244:1568-1576. [PMID: 31594404 PMCID: PMC6920669 DOI: 10.1177/1535370219881129] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Since their discovery just over 25 years ago, the single variable domain from heavy-chain-only antibodies plays a role in an increasing number of antibody-based applications. Structural and biophysical studies have revealed that the small, ∼15 kDa, single variable domain found in camelids displays versatility in target recognition. Such insight has served as the foundation to develop and engineer VHH domains with enhanced properties capable of targeting a range of therapeutically relevant protein antigens or low-molecular weight haptens. Furthermore, the modular nature of VHH domains allows them to be introduced into constructs that are simply not possible with conventional antibodies. Here, we review the structural and biophysical properties of VHH domains, highlight recent VHH-based therapeutics and diagnostics, and provide insight into VHH engineering that may pave the way to next-generation single domain antibody applications.
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Affiliation(s)
- Robert J Hoey
- Department of Chemistry and Biochemistry,
Northern
Illinois University, DeKalb, IL 60115,
USA
| | - Hyeyoung Eom
- Department of Chemistry and Biochemistry,
Northern
Illinois University, DeKalb, IL 60115,
USA
| | - James R Horn
- Department of Chemistry and Biochemistry,
Northern
Illinois University, DeKalb, IL 60115,
USA
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15
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Ali A, Baby B, Vijayan R. From Desert to Medicine: A Review of Camel Genomics and Therapeutic Products. Front Genet 2019; 10:17. [PMID: 30838017 PMCID: PMC6389616 DOI: 10.3389/fgene.2019.00017] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Camels have an important role in the lives of human beings, especially in arid regions, due to their multipurpose role and unique ability to adapt to harsh conditions. In spite of its enormous economic, cultural, and biological importance, the camel genome has not been widely studied. The size of camel genome is roughly 2.38 GB, containing over 20,000 genes. The unusual genetic makeup of the camel is the main reason behind its ability to survive under extreme environmental conditions. The camel genome harbors several unique variations which are being investigated for the treatment of several disorders. Various natural products from camels have also been tested and prescribed as adjunct therapy to control the progression of ailments. Interestingly, the camel employs unique immunological and molecular mechanisms against pathogenic agents and pathological conditions. Here, we broadly review camel classification, distribution and breed as well as recent progress in the determination of the camel genome, its size, genetic distribution, response to various physiological conditions, immunogenetics and the medicinal potential of camel gene products.
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Affiliation(s)
| | | | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
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16
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Salvador JP, Vilaplana L, Marco MP. Nanobody: outstanding features for diagnostic and therapeutic applications. Anal Bioanal Chem 2019; 411:1703-1713. [PMID: 30734854 DOI: 10.1007/s00216-019-01633-4] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/16/2019] [Accepted: 01/21/2019] [Indexed: 11/28/2022]
Abstract
Nanobodies (Nbs) have arisen as an alternative to conventional antibodies (Abs) and show great potential when used as tools in different biotechnology fields such as diagnostics and therapy. Different approaches have been described for the production of Nbs and these methods face new challenges focused on improving yield, affinity, and reducing production costs. This review summarizes these challenges, and also the latest advances in the detection of different kinds of molecules, such as proteins and small molecules, and describes their potential use for noninvasive in vivo imaging and for in vitro assays. Moreover, the unique properties of Nbs are outlined like internalization, size, thermal and chemical stability, affinity, blood clearance, and labeling procedures. Concerning therapeutic applications, we highlight some already reported examples about Nbs being used for the treatment of several diseases such as cancer, neurodegenerative or infectious diseases among others. Finally, future trends, opportunities, and disadvantages are also discussed.
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Affiliation(s)
- J-Pablo Salvador
- Nanobiotechnology for Diagnostics Group (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034, Barcelona, Spain.
| | - Lluïsa Vilaplana
- Nanobiotechnology for Diagnostics Group (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - M-Pilar Marco
- Nanobiotechnology for Diagnostics Group (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034, Barcelona, Spain
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17
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Wang K, Liu Z, Ding G, Li J, Vasylieva N, Li QX, Li D, Gee SJ, Hammock BD, Xu T. Development of a one-step immunoassay for triazophos using camel single-domain antibody-alkaline phosphatase fusion protein. Anal Bioanal Chem 2019; 411:1287-1295. [PMID: 30706076 DOI: 10.1007/s00216-018-01563-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/14/2018] [Accepted: 12/20/2018] [Indexed: 01/17/2023]
Abstract
Triazophos is mainly used in Asian and African countries for the control of insects in agricultural production. Camelid variable domains of heavy-chain antibodies (VHHs) show great promise in monitoring environmental chemicals such as pesticides. To improve the rate of success in the generation of VHHs against triazophos, genes specifically encoding VHH fragments from the unique allotype IgG3a of an immunized Camelus bactrianus were amplified by using a pair of novel primers and introduced to construct a diverse VHH library. Five out of seven isolated positive clones, including the VHH T1 with the highest affinity to triazophos, were derived from the allotype IgG3a. A one-step enzyme-linked immunosorbent assay (ELISA) using VHH T1 genetically fused with alkaline phosphatase (AP) had a half-maximum inhibition concentration of 6.6 ng/mL for triazophos. This assay showed negligible cross-reactivity with a list of important organophosphate pesticides (< 0.1%). The average recoveries of triazophos from water, soil, and apple samples determined by the one-step ELISA ranged from 83 to 108%, having a good correlation with those by a gas chromatography mass spectrometry (R2 = 0.99). The VHH-AP fusion protein shows potential for the analysis of triazophos in various matrices.
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Affiliation(s)
- Kai Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhiping Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Guochun Ding
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Ji Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Natalia Vasylieva
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, 96 Briggs Hall, Davis, CA, 95616, USA
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI, 96822, USA
| | - Dongyang Li
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, 96 Briggs Hall, Davis, CA, 95616, USA
| | - Shirley J Gee
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, 96 Briggs Hall, Davis, CA, 95616, USA
| | - Bruce D Hammock
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, 96 Briggs Hall, Davis, CA, 95616, USA
| | - Ting Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Resources and Environmental Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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18
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Martin-Eauclaire MF, Adi-Bessalem S, Hammoudi-Triki D, Laraba-Djebari F, Bougis PE. Serotherapy against Voltage-Gated Sodium Channel-Targeting αToxins from Androctonus Scorpion Venom. Toxins (Basel) 2019; 11:toxins11020063. [PMID: 30678116 PMCID: PMC6410273 DOI: 10.3390/toxins11020063] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 12/12/2022] Open
Abstract
Because of their venom lethality towards mammals, scorpions of the Androctonus genus are considered a critical threat to human health in North Africa. Several decades of exploration have led to a comprehensive inventory of their venom components at chemical, pharmacological, and immunological levels. Typically, these venoms contain selective and high affinity ligands for the voltage-gated sodium (Nav) and potassium (Kv) channels that dictate cellular excitability. In the well-studied Androctonus australis and Androctonus mauretanicus venoms, almost all the lethality in mammals is due to the so-called α-toxins. These peptides commonly delay the fast inactivation process of Nav channels, which leads to increased sodium entry and a subsequent cell membrane depolarization. Markedly, their neutralization by specific antisera has been shown to completely inhibit the venom’s lethal activity, because they are not only the most abundant venom peptide but also the most fatal. However, the structural and antigenic polymorphisms in the α-toxin family pose challenges to the design of efficient serotherapies. In this review, we discuss past and present accomplishments to improve serotherapy against Androctonus scorpion stings.
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Affiliation(s)
| | - Sonia Adi-Bessalem
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, El-Alia Bab Ezzouar, 16111 Algiers, Algeria.
| | - Djelila Hammoudi-Triki
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, El-Alia Bab Ezzouar, 16111 Algiers, Algeria.
| | - Fatima Laraba-Djebari
- Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, El-Alia Bab Ezzouar, 16111 Algiers, Algeria.
| | - Pierre E Bougis
- Laboratory of Cognitive Neuroscience, CNRS, Aix Marseille Univ, UMR 7291, 13003 Marseille, France.
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19
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Peltomaa R, Glahn-Martínez B, Benito-Peña E, Moreno-Bondi MC. Optical Biosensors for Label-Free Detection of Small Molecules. SENSORS (BASEL, SWITZERLAND) 2018; 18:E4126. [PMID: 30477248 PMCID: PMC6308632 DOI: 10.3390/s18124126] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022]
Abstract
Label-free optical biosensors are an intriguing option for the analyses of many analytes, as they offer several advantages such as high sensitivity, direct and real-time measurement in addition to multiplexing capabilities. However, development of label-free optical biosensors for small molecules can be challenging as most of them are not naturally chromogenic or fluorescent, and in some cases, the sensor response is related to the size of the analyte. To overcome some of the limitations associated with the analysis of biologically, pharmacologically, or environmentally relevant compounds of low molecular weight, recent advances in the field have improved the detection of these analytes using outstanding methodology, instrumentation, recognition elements, or immobilization strategies. In this review, we aim to introduce some of the latest developments in the field of label-free optical biosensors with the focus on applications with novel innovations to overcome the challenges related to small molecule detection. Optical label-free methods with different transduction schemes, including evanescent wave and optical fiber sensors, surface plasmon resonance, surface-enhanced Raman spectroscopy, and interferometry, using various biorecognition elements, such as antibodies, aptamers, enzymes, and bioinspired molecularly imprinted polymers, are reviewed.
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Affiliation(s)
- Riikka Peltomaa
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Bettina Glahn-Martínez
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Elena Benito-Peña
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - María C Moreno-Bondi
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
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20
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A Two-Step Approach for the Design and Generation of Nanobodies. Int J Mol Sci 2018; 19:ijms19113444. [PMID: 30400198 PMCID: PMC6274671 DOI: 10.3390/ijms19113444] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/29/2022] Open
Abstract
Nanobodies, the smallest possible antibody format, have become of considerable interest for biotechnological and immunotherapeutic applications. They show excellent robustness, are non-immunogenic in humans, and can easily be engineered and produced in prokaryotic hosts. Traditionally, nanobodies are selected from camelid immune libraries involving the maintenance and treatment of animals. Recent advances have involved the generation of nanobodies from naïve or synthetic libraries. However, such approaches demand large library sizes and sophisticated selection procedures. Here, we propose an alternative, two-step approach for the design and generation of nanobodies. In a first step, complementarity-determining regions (CDRs) are grafted from conventional antibody formats onto nanobody frameworks, generating weak antigen binders. In a second step, the weak binders serve as templates to design focused synthetic phage libraries for affinity maturation. We validated this approach by grafting toxin- and hapten-specific CDRs onto frameworks derived from variable domains of camelid heavy-chain-only antibodies (VHH). We then affinity matured the hapten binder via panning of a synthetic phage library. We suggest that this strategy can complement existing immune, naïve, and synthetic library based methods, requiring neither animal experiments, nor large libraries, nor sophisticated selection protocols.
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21
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Tabares-da Rosa S, Wogulis LA, Wogulis MD, González-Sapienza G, Wilson DK. Structure and specificity of several triclocarban-binding single domain camelid antibody fragments. J Mol Recognit 2018; 32:e2755. [PMID: 30033524 DOI: 10.1002/jmr.2755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 12/29/2022]
Abstract
The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. A high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions. Additional significant interactions are formed with a non-hypervariable loop, sometimes dubbed "CDR4". A comparison of apo and holo forms of T9 and T10 shows that the binding site undergoes little conformational change upon binding of TCC. Structures of three nanobody-TCC complexes demonstrated there was not a standard binding mode. T4 and T9 have a high degree of sequence identity and bind the hapten in a nearly identical manner, while the more divergent T10 binds TCC in a slightly displaced orientation with the urea moiety rotated approximately 180° along the long axis of the molecule. In addition to methotrexate, this is the second report of haptens binding in a tunnel formed by CDR1, suggesting that compounds with similar hydrophobicity and shape could be recognized by nanobodies in analogous fashion. Structure-guided mutations failed to improve binding affinity for T4 and T9 underscoring the high degree of natural optimization.
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Affiliation(s)
| | - Linda A Wogulis
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Mark D Wogulis
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | | | - David K Wilson
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
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22
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He T, Zhu J, Nie Y, Hu R, Wang T, Li P, Zhang Q, Yang Y. Nanobody Technology for Mycotoxin Detection in the Field of Food Safety: Current Status and Prospects. Toxins (Basel) 2018; 10:E180. [PMID: 29710823 PMCID: PMC5983236 DOI: 10.3390/toxins10050180] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 01/18/2023] Open
Abstract
Mycotoxins, which are toxic, carcinogenic, and/or teratogenic, have posed a threat to food safety and public health. Sensitive and effective determination technologies for mycotoxin surveillance are required. Immunoassays have been regarded as useful supplements to chromatographic techniques. However, conventional antibodies involved in immunoassays are difficult to be expressed recombinantly and are susceptible to harsh environments. Nanobodies (or VHH antibodies) are antigen-binding sites of the heavy-chain antibodies produced from Camelidae. They are found to be expressed easily in prokaryotic or eukaryotic expression systems, more robust in extreme conditions, and facile to be used as surrogates for artificial antigens. These properties make them the promising and environmentally friendly immunoreagents in the next generation of immunoassays. This review briefly describes the latest developments in the area of nanobodies used in mycotoxin detection. Moreover, by integrating the introduction of the principle of nanobodies production and the critical assessment of their performance, this paper also proposes the prospect of nanobodies in the field of food safety in the foreseeable future.
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Affiliation(s)
- Ting He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Ting Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Peiwu Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Qi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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23
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Yerabham ASK, Müller-Schiffmann A, Ziehm T, Stadler A, Köber S, Indurkhya X, Marreiros R, Trossbach SV, Bradshaw NJ, Prikulis I, Willbold D, Weiergräber OH, Korth C. Biophysical insights from a single chain camelid antibody directed against the Disrupted-in-Schizophrenia 1 protein. PLoS One 2018; 13:e0191162. [PMID: 29324815 PMCID: PMC5764400 DOI: 10.1371/journal.pone.0191162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/31/2017] [Indexed: 01/17/2023] Open
Abstract
Accumulating evidence suggests an important role for the Disrupted-in-Schizophrenia 1 (DISC1) protein in neurodevelopment and chronic mental illness. In particular, the C-terminal 300 amino acids of DISC1 have been found to mediate important protein-protein interactions and to harbor functionally important phosphorylation sites and disease-associated polymorphisms. However, long disordered regions and oligomer-forming subdomains have so far impeded structural analysis. VHH domains derived from camelid heavy chain only antibodies are minimal antigen binding modules with appreciable solubility and stability, which makes them well suited for the stabilizing proteins prior to structural investigation. Here, we report on the generation of a VHH domain derived from an immunized Lama glama, displaying high affinity for the human DISC1 C region (aa 691-836), and its characterization by surface plasmon resonance, size exclusion chromatography and immunological techniques. The VHH-DISC1 (C region) complex was also used for structural investigation by small angle X-ray scattering analysis. In combination with molecular modeling, these data support predictions regarding the three-dimensional fold of this DISC1 segment as well as its steric arrangement in complex with our VHH antibody.
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Affiliation(s)
- Antony S. K. Yerabham
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Tamar Ziehm
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS, Forschungszentrum Jülich, Jülich, Germany
| | - Sabrina Köber
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Xela Indurkhya
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rita Marreiros
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Svenja V. Trossbach
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicholas J. Bradshaw
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingrid Prikulis
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute for Physical Biology and BMFZ, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver H. Weiergräber
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Carsten Korth
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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24
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Scholler P, Nevoltris D, de Bundel D, Bossi S, Moreno-Delgado D, Rovira X, Møller TC, El Moustaine D, Mathieu M, Blanc E, McLean H, Dupuis E, Mathis G, Trinquet E, Daniel H, Valjent E, Baty D, Chames P, Rondard P, Pin JP. Allosteric nanobodies uncover a role of hippocampal mGlu2 receptor homodimers in contextual fear consolidation. Nat Commun 2017; 8:1967. [PMID: 29213077 PMCID: PMC5719040 DOI: 10.1038/s41467-017-01489-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/15/2017] [Indexed: 11/09/2022] Open
Abstract
Antibodies have enormous therapeutic and biotechnology potential. G protein-coupled receptors (GPCRs), the main targets in drug development, are of major interest in antibody development programs. Metabotropic glutamate receptors are dimeric GPCRs that can control synaptic activity in a multitude of ways. Here we identify llama nanobodies that specifically recognize mGlu2 receptors, among the eight subtypes of mGluR subunits. Among these nanobodies, DN10 and 13 are positive allosteric modulators (PAM) on homodimeric mGlu2, while DN10 displays also a significant partial agonist activity. DN10 and DN13 have no effect on mGlu2-3 and mGlu2-4 heterodimers. These PAMs enhance the inhibitory action of the orthosteric mGlu2/mGlu3 agonist, DCG-IV, at mossy fiber terminals in the CA3 region of hippocampal slices. DN13 also impairs contextual fear memory when injected in the CA3 region of hippocampal region. These data highlight the potential of developing antibodies with allosteric actions on GPCRs to better define their roles in vivo.
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Affiliation(s)
- Pauline Scholler
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
- Cisbio Bioassays, F-30200, Codolet, France
| | - Damien Nevoltris
- Cisbio Bioassays, F-30200, Codolet, France
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, F-13009, Marseille, France
| | - Dimitri de Bundel
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Simon Bossi
- CNRS UMR9197, Université Paris-Sud, Institut des Neurosciences Paris-Saclay, F-91405, Orsay, France
| | - David Moreno-Delgado
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Xavier Rovira
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Thor C Møller
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Driss El Moustaine
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Michaël Mathieu
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Emilie Blanc
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Heather McLean
- CNRS UMR9197, Université Paris-Sud, Institut des Neurosciences Paris-Saclay, F-91405, Orsay, France
| | | | | | | | - Hervé Daniel
- CNRS UMR9197, Université Paris-Sud, Institut des Neurosciences Paris-Saclay, F-91405, Orsay, France
| | - Emmanuel Valjent
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Daniel Baty
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, F-13009, Marseille, France
| | - Patrick Chames
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, F-13009, Marseille, France.
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France.
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France.
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Liu Y, Huang H. Expression of single-domain antibody in different systems. Appl Microbiol Biotechnol 2017; 102:539-551. [DOI: 10.1007/s00253-017-8644-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/09/2017] [Accepted: 11/12/2017] [Indexed: 10/18/2022]
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Pírez-Schirmer M, Rossotti M, Badagian N, Leizagoyen C, Brena BM, González-Sapienza G. Comparison of Three Antihapten VHH Selection Strategies for the Development of Highly Sensitive Immunoassays for Microcystins. Anal Chem 2017; 89:6800-6806. [PMID: 28494149 DOI: 10.1021/acs.analchem.7b01221] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Owing to their reproducibility, stability, and cost-effective production, the recombinant variable domains of heavy-chain-only antibodies (VHHs) are becoming a salient option as immunoassay reagents. Recently, there have been several reports describing their application to the detection of small molecules (haptens). However, lacking the heavy-light chain interface of conventional antibodies, VHHs are not particularly apt to bind small analytes and failures are not uncommon. Here we describe the construction of a VHH phage display library against the cyanobacterial hepatotoxin microcystin LR and its selection using competitive panning and two novel panning strategies. The outcome of each strategy was evaluated by a large-scale screening using in vivo biotinylated nanobodies. The three methods selected for different nonoverlapping subsets of VHHs, allowing one to optimize the immunodetection of the toxin. The best results were obtained by promoting the isolation of VHHs with the slowest koff (off-rate selection). Among these, the biotinylated nanobody A2.3 performed in ELISA with excellent recovery and high sensitivity, IC50 = 0.28 μg/L, with a limit of detection that is well below the most rigorous guidelines for the toxin. While it may be case-specific, these results highlight the importance of exploring different panning strategies to optimize the selection of antihapten nanobodies.
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Affiliation(s)
| | | | | | - Carmen Leizagoyen
- Parque Lecocq, Intendencia de Montevideo , Montevideo, Uruguay , 12600
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27
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Al Qaraghuli MM, Ferro VA. Analysis of the binding loops configuration and surface adaptation of different crystallized single-domain antibodies in response to various antigens. J Mol Recognit 2016; 30. [PMID: 27862476 DOI: 10.1002/jmr.2592] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/10/2016] [Accepted: 10/23/2016] [Indexed: 11/08/2022]
Abstract
Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes.
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Affiliation(s)
- Mohammed M Al Qaraghuli
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Valerie A Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
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Bever CS, Dong JX, Vasylieva N, Barnych B, Cui Y, Xu ZL, Hammock BD, Gee SJ. VHH antibodies: emerging reagents for the analysis of environmental chemicals. Anal Bioanal Chem 2016; 408:5985-6002. [PMID: 27209591 DOI: 10.1007/s00216-016-9585-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 01/28/2023]
Abstract
A VHH antibody (or nanobody) is the antigen binding fragment of heavy chain only antibodies. Discovered nearly 25 years ago, they have been investigated for their use in clinical therapeutics and immunodiagnostics, and more recently for environmental monitoring applications. A new and valuable immunoreagent for the analysis of small molecular weight environmental chemicals, VHH will overcome many pitfalls encountered with conventional reagents. In the work so far, VHH antibodies often perform comparably to conventional antibodies for small molecule analysis, are amenable to numerous genetic engineering techniques, and show ease of adaption to other immunodiagnostic platforms for use in environmental monitoring. Recent reviews cover the structure and production of VHH antibodies as well as their use in clinical settings. However, no report focuses on the use of these VHH antibodies to detect small environmental chemicals (MW < 1500 Da). This review article summarizes the efforts made to produce VHHs to various environmental targets, compares the VHH-based assays with conventional antibody assays, and discusses the advantages and limitations in developing these new antibody reagents particularly to small molecule targets. Graphical Abstract Overview of the production of VHHs to small environmental chemicals and highlights of the utility of these new emerging reagents.
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Affiliation(s)
- Candace S Bever
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jie-Xian Dong
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Natalia Vasylieva
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Bogdan Barnych
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Yongliang Cui
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.,Department of Oral Biology, School of Dental Medicine, University of Buffalo, State University of New York, Buffalo, NY, 14214, USA
| | - Zhen-Lin Xu
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Shirley J Gee
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
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Davenport KR, Smith CA, Hofstetter H, Horn JR, Hofstetter O. Site-directed immobilization of a genetically engineered anti-methotrexate antibody via an enzymatically introduced biotin label significantly increases the binding capacity of immunoaffinity columns. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:114-121. [PMID: 26809205 DOI: 10.1016/j.jchromb.2016.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
In this study, the effect of random vs. site-directed immobilization techniques on the performance of antibody-based HPLC columns was investigated using a single-domain camelid antibody (VHH) directed against methotrexate (MTX) as a model system. First, the high flow-through support material POROS-OH was activated with disuccinimidyl carbonate (DSC), and the VHH was bound in a random manner via amines located on the protein's surface. The resulting column was characterized by Frontal Affinity Chromatography (FAC). Then, two site-directed techniques were explored to increase column efficiency by immobilizing the antibody via its C-terminus, i.e., away from the antigen-binding site. In one approach, a tetra-lysine tail was added, and the antibody was immobilized onto DSC-activated POROS. In the second site-directed approach, the VHH was modified with the AviTag peptide, and a biotin-residue was enzymatically incorporated at the C-terminus using the biotin ligase BirA. The biotinylated antibody was subsequently immobilized onto NeutrAvidin-derivatized POROS. A comparison of the FAC analyses, which for all three columns showed excellent linearity (R(2)>0.999), revealed that both site-directed approaches yield better results than the random immobilization; the by far highest efficiency, however, was determined for the immunoaffinity column based on AviTag-biotinylated antibody. As proof of concept, all three columns were evaluated for quantification of MTX dissolved in phosphate buffered saline (PBS). Validation using UV-detection showed excellent linearity in the range of 0.04-12μM (R(2)>0.993). The lower limit of detection (LOD) and lower limit of quantification (LLOQ) were found to be independent of the immobilization strategy and were 40nM and 132nM, respectively. The intra- and inter-day precision was below 11.6%, and accuracy was between 90.7% and 112%. To the best of our knowledge, this is the first report of the AviTag-system in chromatography, and the first application of immunoaffinity chromatography for the analysis of MTX.
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Affiliation(s)
- Kaitlynn R Davenport
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Christopher A Smith
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Heike Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Oliver Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA.
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30
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Xu B, Zhou X, Stains CI. Supramolecular Assembly of an Evolved Miniprotein Host and Fluorogenic Guest Pair. J Am Chem Soc 2015; 137:14252-5. [DOI: 10.1021/jacs.5b09494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bi Xu
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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Optimization of dilution refolding conditions for a camelid single domain antibody against human beta-2-microglobulin. Protein Expr Purif 2015; 117:59-66. [PMID: 26386406 DOI: 10.1016/j.pep.2015.09.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 01/11/2023]
Abstract
Single domain antibody (sdAb) is often expressed as inclusion bodies in Escherichia coli cytoplasm. Establishing an effective in vitro refolding method for sdAb obtained from inclusion bodies would be important for sdAb research. In this study, dilution refolding condition for a camelid sdAb specific against human beta-2-microglobulin was optimized for the sdAb purified from the inclusion bodies of E. coli BL21 (DE3). Single factor methods based on protein concentration, velocity of dilution, incubation time and refolding buffer composition were first investigated. Then the key refolding buffer compositions were selected for further optimization by means of the Box-Behnken design of response surface methodology (RSM). The activity of the refolded sdAb was determined by measuring its specific antigen-binding ability using indirect ELISA. The optimized refolding condition of sdAb consisted of a 10-fold dilution in 10 mM Tris-HCl (pH 8.0) containing 1.24 mM GSH, 1mM GSSG, 352 mM L-Arg, 0.65% PEG-2000, and a 16 h incubation at 4 °C. Further comparison of the activities between the refolded sdAb and purified soluble sdAb expressed in E. coli Rosetta-gami (DE3) pLysS indicated that the sdAb was correctly refolded, as assayed by isothermal titration calorimetry. This work could provide an important strategy for the recombinant production and application of sdAb.
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32
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Rousserie G, Grinevich R, Brazhnik K, Even-Desrumeaux K, Reveil B, Tabary T, Chames P, Baty D, Cohen JH, Nabiev I, Sukhanova A. Detection of carcinoembryonic antigen using single-domain or full-size antibodies stained with quantum dot conjugates. Anal Biochem 2015; 478:26-32. [DOI: 10.1016/j.ab.2015.02.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 02/23/2015] [Accepted: 02/28/2015] [Indexed: 12/18/2022]
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33
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Kavanagh O, Elliott CT, Campbell K. Progress in the development of immunoanalytical methods incorporating recombinant antibodies to small molecular weight biotoxins. Anal Bioanal Chem 2015; 407:2749-70. [PMID: 25716465 DOI: 10.1007/s00216-015-8502-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/08/2023]
Abstract
Rapid immunoanalytical screening of food and environmental samples for small molecular weight (hapten) biotoxin contaminations requires the production of antibody reagents that possess the requisite sensitivity and specificity. To date animal-derived polyclonal (pAb) and monoclonal (mAb) antibodies have provided the binding element of the majority of these assays but recombinant antibodies (rAb) isolated from in vitro combinatorial phage display libraries are an exciting alternative due to (1) circumventing the need for experimental animals, (2) speed of production in commonly used in vitro expression systems and (3) subsequent molecular enhancement of binder performance. Short chain variable fragments (scFv) have been the most commonly employed rAb reagents for hapten biotoxin detection over the last two decades but antibody binding fragments (Fab) and single domain antibodies (sdAb) are increasing in popularity due to increased expression efficiency of functional binders and superior resistance to solvents. rAb-based immunochromatographic assays and surface plasmon resonance (SPR) biosensors have been reported to detect sub-regulatory levels of fungal (mycotoxins), marine (phycotoxins) and aquatic biotoxins in a wide range of food and environmental matrices, however this technology has yet to surpass the performances of the equivalent mAb- and pAb-based formats. As such the full potential of rAb technology in hapten biotoxin detection has yet to be achieved, but in time the inherent advantages of engineered rAb are set to provide the next generation of ultra-high performing binder reagents for the rapid and specific detection of hapten biotoxins.
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Affiliation(s)
- Owen Kavanagh
- Institute for Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK,
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34
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Nevoltris D, Lombard B, Dupuis E, Mathis G, Chames P, Baty D. Conformational nanobodies reveal tethered epidermal growth factor receptor involved in EGFR/ErbB2 predimers. ACS NANO 2015; 9:1388-1399. [PMID: 25603171 DOI: 10.1021/nn505752u] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The epidermal growth factor receptor (EGFR) is a cell-surface receptor with a single transmembrane domain and tyrosine kinase activity carried by the intracellular domain. This receptor is one of the four members of the ErbB family including ErbB2, ErbB3, and ErbB4. Ligand binding, like EGF binding, induces a conformational rearrangement of the receptor and induces a homo/hetero dimerization essentially with ErbB family receptors that leads to the phosphorylation of the kinase domain, triggering a signaling cascade. EGFR can also form inactive dimers in a ligand-independent way through interactions between cytoplasmic domains. To date, the conformation of EGFR extracellular domain engaged in these inactive dimers remains unclear. In this study, we describe the successful selection and characterization of llama anti-EGFR nanobodies and their use as innovative conformational sensors. We isolated three different specific anti-EGFR clones binding to three distinct epitopes. Interestingly, the binding of all three nanobodies was found highly sensitive to ligand stimulation. Two nanobodies, D10 and E10, can only bind the ligand-free EGFR conformation characterized by an intramolecular tether between domains II and IV, whereas nanobody G10 binds both ligand-free and ligand activated EGFR, with an 8-fold higher affinity for the extended conformation in the presence of ligand. Here we took advantage of these conformational probes to reveal the existence of tethered EGFR in EGFR/ErbB2 predimers. These biosensors represent important tools allowing the determination of EGFR conformations and should help the design of relevant inhibitors.
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Affiliation(s)
- Damien Nevoltris
- Institut National de la Santé et de la Recherche Médicale , U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France
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35
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Fridy PC, Li Y, Keegan S, Thompson MK, Nudelman I, Scheid JF, Oeffinger M, Nussenzweig MC, Fenyö D, Chait BT, Rout MP. A robust pipeline for rapid production of versatile nanobody repertoires. Nat Methods 2014; 11:1253-60. [PMID: 25362362 PMCID: PMC4272012 DOI: 10.1038/nmeth.3170] [Citation(s) in RCA: 361] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 09/25/2014] [Indexed: 12/18/2022]
Abstract
Nanobodies are single-domain antibodies derived from the variable regions of Camelidae atypical immunoglobulins. They show promise as high-affinity reagents for research, diagnostics and therapeutics owing to their high specificity, small size (∼15 kDa) and straightforward bacterial expression. However, identification of repertoires with sufficiently high affinity has proven time consuming and difficult, hampering nanobody implementation. Our approach generates large repertoires of readily expressible recombinant nanobodies with high affinities and specificities against a given antigen. We demonstrate the efficacy of this approach through the production of large repertoires of nanobodies against two antigens, GFP and mCherry, with Kd values into the subnanomolar range. After mapping diverse epitopes on GFP, we were also able to design ultrahigh-affinity dimeric nanobodies with Kd values as low as ∼30 pM. The approach presented here is well suited for the routine production of high-affinity capture reagents for various biomedical applications.
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Affiliation(s)
- Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Yinyin Li
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Sarah Keegan
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA
| | - Mary K Thompson
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Ilona Nudelman
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Marlene Oeffinger
- 1] Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada. [2] Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montreal, Quebec, Canada
| | - Michel C Nussenzweig
- 1] Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA. [2] Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
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36
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Zare H, Rajabibazl M, Rasooli I, Ebrahimizadeh W, Bakherad H, Ardakani LS, Gargari SLM. Production of nanobodies against prostate-specific membrane antigen (PSMA) recognizing LnCaP cells. Int J Biol Markers 2014; 29:e169-e179. [PMID: 24425321 DOI: 10.5301/jbm.5000063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2013] [Indexed: 12/17/2022]
Abstract
Prostate cancer is the most common type of cancer in men. The antibody-mediated therapy for cancer treatment depends on the identification of selected molecular targets. The prostate-specific membrane antigen (PSMA) is a potential molecular target in prostate cancer and is abundantly expressed in this type of cancer. This study is aimed at designing and producing a recombinant PSMA epitope and a monoclonal nanobody with a high affinity toward the PSMA protein. A DNA fragment encoding the dominant epitopes of PSMA was designed, synthesized, and expressed in E. coli BL21 (DE3). A camel was immunized with the purified recombinant PSMA (rPSMA). Following mRNA isolation and cDNA synthesis, the variable fragment of heavy-chain antibodies (VHH) fragments were cloned and displayed on the surface of an M13 phage and used in sequential panning rounds. After phage ELISA and selection of colonies with the highest affinity, soluble nanobodies were produced and evaluated. Affinity of the nanobodies to rPSMA was estimated to be 3.5 × 10-7. Adherence of the purified anti-PSMA VHH was tested in cell-ELISA in the LnCaP and PC3 cell lines. VHH efficiently bound to LnCaP cells. The high specificity and affinity of this nanobody suggests its possible application as an effective tool in the diagnosis and treatment of prostate cancer.
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Affiliation(s)
- Hamed Zare
- Department of Biology, Faculty of Basic Science, Shahed University, Tehran - Iran
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Fatima A, Wang H, Kang K, Xia L, Wang Y, Ye W, Wang J, Wang X. Development of VHH antibodies against dengue virus type 2 NS1 and comparison with monoclonal antibodies for use in immunological diagnosis. PLoS One 2014; 9:e95263. [PMID: 24751715 PMCID: PMC3994031 DOI: 10.1371/journal.pone.0095263] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/25/2014] [Indexed: 11/22/2022] Open
Abstract
The possibility of using variable domain heavy-chain antibodies (VHH antibodies) as diagnostic tools for dengue virus (DENV) type 2 NS1 protein was investigated and compared with the use of conventional monoclonal antibodies. After successful expression of DENV type 2 NS1 protein, the genes of VHH antibodies against NS1 protein were biopanned from a non-immune llama library by phage display. VHH antibodies were then expressed and purified from Escherichia coli. Simultaneously, monoclonal antibodies were obtained by the conventional route. Sequence analysis of the VHH antibodies revealed novel and long complementarity determining regions 3 (CDR3). Epitope mapping was performed via a phage display peptide library using purified VHH and monoclonal antibodies as targets. Interestingly, the same region of NS1, which comprises amino acids 224HWPKPHTLW232, was conserved for both kinds of antibodies displaying the consensus motif histidine-tryptophan-tryptophan or tryptophan-proline-tryptophan. The two types of antibodies were used to prepare rapid diagnostic kits based on immunochromatographic assay. The VHH antibody immobilized rapid diagnostic kit showed better sensitivity and specificity than the monoclonal antibody immobilized rapid diagnostic kit, which might be due to the long CDR3 regions of the VHH antibodies and their ability to bind to the pocket and cleft of the targeted antigen. This demonstrates that VHH antibodies are likely to be an option for developing point-of-care tests against DENV infection.
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Affiliation(s)
- Aneela Fatima
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, PR China
| | - Haiying Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, PR China
| | - Keren Kang
- Guangzhou Wondfo Biotech Co., Ltd, Scientific City, Guangzhou, PR China
| | - Liliang Xia
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, PR China
| | - Ying Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, PR China
| | - Wei Ye
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, PR China
| | - Jufang Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, PR China
| | - Xiaoning Wang
- Institute of Life Science, General Hospital of The People’s Liberation Army, Beijing, PR China
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Sharifzadeh Z, Rahbarizadeh F, Shokrgozar MA, Ahmadvand D, Mahboudi F, Rahimi Jamnani F, Aghaee Bakhtiari SH. Development of oligoclonal nanobodies for targeting the tumor-associated glycoprotein 72 antigen. Mol Biotechnol 2013; 54:590-601. [PMID: 23015323 DOI: 10.1007/s12033-012-9601-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The tumor-associated glycoprotein 72 (TAG-72) is a membrane mucin whose over-expression is correlated with advanced tumor stage and increased invasion and metastasis. In this study, we identified a panel of four nanobodies, single variable domains of dromedary heavy-chain antibodies that specifically recognize the TAG-72 antigen. All selected nanobodies were shown to selectively bind to this cancer-related molecule with low-nanomolar affinities and do not cross-react with other antigens, such as MUC1 or HER2. Furthermore, they can detect TAG-72 in concentrations as low as 5 U/ml which is valuable in sensitive detection of this molecule in cancerous patients. Cell ELISA experiments proved their ability for binding to the native target antigen on TAG-72 expressing cells while not showing any reactivity to HT-29 cells, a TAG-72-negative cell line. Using competition studies, we found that each nanobody recognizes a distinct epitope on the TAG-72 antigen that is different from the one recognized by the mouse anti-TAG-72 antibody, CC49. Considering their high specificity, reduced immunogenicity and multi-targeting behavior, these oligoclonal nanobodies represent a promising tool to target TAG-72 over-expressing tumor cells.
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Even-Desrumeaux K, Nevoltris D, Lavaut MN, Alim K, Borg JP, Audebert S, Kerfelec B, Baty D, Chames P. Masked selection: a straightforward and flexible approach for the selection of binders against specific epitopes and differentially expressed proteins by phage display. Mol Cell Proteomics 2013; 13:653-65. [PMID: 24361863 DOI: 10.1074/mcp.o112.025486] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Phage display is a well-established procedure to isolate binders against a wide variety of antigens that can be performed on purified antigens, but also on intact cells. As selection steps are performed in vitro, it is possible to focus the outcome of the selection on relevant epitopes by performing some additional steps, such as depletion or competitive elutions. However in practice, the efficiency of these steps is often limited and can lead to inconsistent results. We have designed a new selection method named masked selection, based on the blockade of unwanted epitopes to favor the targeting of relevant ones. We demonstrate the efficiency and flexibility of this method by selecting single-domain antibodies against a specific portion of a fusion protein, by selecting binders against several members of the seven transmembrane receptor family using transfected HEK cells, or by selecting binders against unknown breast cancer markers not expressed on normal samples. The relevance of this approach for antibody-based therapies was further validated by the identification of four of these markers, Epithelial cell adhesion molecule, Transferrin receptor 1, Metastasis cell adhesion molecule, and Sushi containing domain 2, using immunoprecipitation and mass spectrometry. This new phage display strategy can be applied to any type of antibody fragments or alternative scaffolds, and is especially suited for the rapid discovery and identification of cell surface markers.
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Salema V, Fernández LÁ. High yield purification of nanobodies from the periplasm of E. coli as fusions with the maltose binding protein. Protein Expr Purif 2013; 91:42-8. [DOI: 10.1016/j.pep.2013.07.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/02/2013] [Accepted: 07/05/2013] [Indexed: 01/31/2023]
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Minaeian S, Rahbarizadeh F, Zarkesh Esfahani SH, Ahmadvand D. Characterization and enzyme-conjugation of a specific anti-L1 nanobody. J Immunoassay Immunochem 2013; 33:422-34. [PMID: 22963491 DOI: 10.1080/15321819.2012.665407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Persistent infection of the human papillomaviruses (HPV) has been shown to result in cervical cancer and intraepithelial neoplasia. Early detection and screening programs are essential strategies against cervical cancer. A nanobody is the smallest antigen-binding fragment known and is derived from a camelid heavy-chain antibody. This tiny protein shows high solubility and stability. It can be produced cost-effectively with high yield production. In this study, we enriched a nanobody library against the L1 protein of HPV. Several colons were selected from this enriched library using monoclonal phage-enzyme linked immunosorbent assay (phage-ELISA) and analyzed for identification of nanobody genes. The expression of nanobody fragments was performed in Rosetta gami2. The C74 nanobody that showed strong binding to the L1 protein of HPV16 was selected, purified, and characterized by Western blotting and ELISA. The selected nanobody was tested for sensitivity, specificity, and affinity. A nanobody conjugated to horseradish peroxidase (HRP) was selected and used for detection of L1 protein of HPV16. This study demonstrates that the C74-HRP, due to its specificity and good binding affinity for a specific viral antigen, is a potential diagnostic tool that can be used as a promising reagent for the new generation of HPV diagnosis approaches.
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Affiliation(s)
- Sara Minaeian
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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42
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Oeffinger M. Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes. Proteomics 2012; 12:1591-608. [PMID: 22592981 DOI: 10.1002/pmic.201100509] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cellular functions are defined by the dynamic interactions of proteins within macromolecular networks. Deciphering these complex interplays is the key to getting a comprehensive picture of cellular behavior and to understanding biological systems, from a simple bacterial cell to highly regulated neuronal cells or cancerous tissue. In the last decade, affinity purification (AP) coupled to mass spectrometry has emerged as a powerful tool to comprehensively study interaction networks and their macromolecular assemblies. This review discusses recent advances in AP approaches, from cell lysis to the importance of sample preparation and the choice of AP matrix as well as the development of different epitope tags and strategies to study dynamic interactions, with an emphasis on RNA-protein interaction networks.
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Affiliation(s)
- Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada.
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43
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Even-Desrumeaux K, Fourquet P, Secq V, Baty D, Chames P. Single-domain antibodies: a versatile and rich source of binders for breast cancer diagnostic approaches. MOLECULAR BIOSYSTEMS 2012; 8:2385-94. [PMID: 22772166 DOI: 10.1039/c2mb25063b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Noninvasive early detection of breast cancer through the use of biomarkers is urgently needed since the risk of recurrence, morbidity, and mortality is closely related to disease stage at the time of primary surgery. A crucial issue in this approach is the availability of relevant markers and corresponding monoclonal antibodies suitable for the development of effective immunodiagnostic modalities. The identification of such markers from human pathological lesions and the isolation of specific antibodies using conventional approaches remain major challenges. Camelids produce functional antibodies devoid of light chains in which the single N-terminal domain of the heavy chain is fully capable of antigen binding. When produced as an independent domain, these so-called single-domain antibody fragments (sdAbs) or nanobodies have several advantages for biotechnological applications owing to their unique properties of size (13 kDa), stability, solubility, and expression yield. In this work, we have generated phage display libraries from animals immunized with breast cancer biopsies. These libraries were used to isolate sdAbs against known and relevant antigens such as HER2, or several cancer-specific sdAbs against unknown targets. We describe the identification of one these targets, cytokeratin 19, using affinity purification in combination with mass spectrometry. Some of these sdAbs were used in several straightforward diagnostic applications such as immunohistochemical analysis of tumor samples, multiplexed cytometric bead array analysis of crude samples, or an immune enrichment procedure of rare cells. Here, we demonstrate that phage display-based selection of single-domain antibodies is an efficient and high-throughput compatible approach to generate binders with excellent characteristics for the fast development of diagnostic and prognostic modalities.
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Kim HJ, McCoy MR, Majkova Z, Dechant JE, Gee SJ, Tabares-da Rosa S, González-Sapienza GG, Hammock BD. Isolation of alpaca anti-hapten heavy chain single domain antibodies for development of sensitive immunoassay. Anal Chem 2012; 84:1165-71. [PMID: 22148739 PMCID: PMC3264785 DOI: 10.1021/ac2030255] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Some unique subclasses of Camelidae antibodies are devoid of the light chain, and the antigen binding site is comprised exclusively of the variable domain of the heavy chain (VHH). Although conventional antibodies dominate current assay development, recombinant VHHs have a high potential as alternative reagents for the next generation of immunoassay. We expressed VHHs from an immunized alpaca and developed a VHH-based immunoassay using 3-phenoxybenzoic acid (3-PBA), a major metabolite of pyrethroid insecticides as a model system. A phage VHH library was constructed, and seven VHH clones were selected by competitive binding with 3-PBA. The best immunoassay developed with one of these VHHs showed an IC(50) of 1.4 ng/mL (limit of detection (LOD) = 0.1 ng/mL). These parameters were further improved by using the phage borne VHH, IC(50) = 0.1 ng/mL and LOD = 0.01 ng/mL. Both assays showed a similar tolerance to methanol and dimethylsulfoxide up to 50% in assay buffer. The assay was highly specific to 3-PBA and its 4-hydroxylated derivative, 4-hydroxy 3-PBA, (150% cross reactivity) with negligible cross reactivity with other tested structural analogues, and the recovery from spiked urine sample ranged from 80 to 112%. In conclusion, a highly specific and sensitive VHH for 3-PBA was developed using sequences from immunized alpaca and phage display technology for antibody selection.
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Affiliation(s)
- Hee-Joo Kim
- Department of Entomology and UCD Cancer Center, University of California, Davis, California 95616, United States
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45
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Isolation of a highly thermal stable lama single domain antibody specific for Staphylococcus aureus enterotoxin B. BMC Biotechnol 2011; 11:86. [PMID: 21933444 PMCID: PMC3193169 DOI: 10.1186/1472-6750-11-86] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 09/21/2011] [Indexed: 11/25/2022] Open
Abstract
Background Camelids and sharks possess a unique subclass of antibodies comprised of only heavy chains. The antigen binding fragments of these unique antibodies can be cloned and expressed as single domain antibodies (sdAbs). The ability of these small antigen-binding molecules to refold after heating to achieve their original structure, as well as their diminutive size, makes them attractive candidates for diagnostic assays. Results Here we describe the isolation of an sdAb against Staphyloccocus aureus enterotoxin B (SEB). The clone, A3, was found to have high affinity (Kd = 75 pM) and good specificity for SEB, showing no cross reactivity to related molecules such as Staphylococcal enterotoxin A (SEA), Staphylococcal enterotoxin D (SED), and Shiga toxin. Most remarkably, this anti-SEB sdAb had an extremely high Tm of 85°C and an ability to refold after heating to 95°C. The sharp Tm determined by circular dichroism, was found to contrast with the gradual decrease observed in intrinsic fluorescence. We demonstrated the utility of this sdAb as a capture and detector molecule in Luminex based assays providing limits of detection (LODs) of at least 64 pg/mL. Conclusion The anti-SEB sdAb A3 was found to have a high affinity and an extraordinarily high Tm and could still refold to recover activity after heat denaturation. This combination of heat resilience and strong, specific binding make this sdAb a good candidate for use in antibody-based toxin detection technologies.
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Tabares-da Rosa S, Rossotti M, Carleiza C, Carrión F, Pritsch O, Ahn KC, Last JA, Hammock BD, González-Sapienza G. Competitive selection from single domain antibody libraries allows isolation of high-affinity antihapten antibodies that are not favored in the llama immune response. Anal Chem 2011; 83:7213-20. [PMID: 21827167 DOI: 10.1021/ac201824z] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-domain antibodies (sdAbs) found in camelids lack a light chain, and their antigen-binding site sits completely in the heavy-chain variable domain (VHH). Their simplicity, thermostability, and ease in expression have made VHHs highly attractive. Although this has been successfully exploited for macromolecular antigens, their application to the detection of small molecules is still limited to a very few reports, mostly describing low-affinity VHHs. Using triclocarban (TCC) as a model hapten, we found that conventional antibodies, IgG1 fraction, reacted with free TCC with a higher relative affinity (IC(50) 51.0 ng/mL) than did the sdAbs (IgG2 and IgG3, 497 and 370 ng/mL, respectively). A VHH library was prepared, and by elution of phage with limiting concentrations of TCC and competitive selection of binders, we were able to isolate high-affinity clones, K(D) 0.98-1.37 nM (SPR), which allowed development of a competitive assay for TCC with an IC(50) = 3.5 ng/mL (11 nM). This represents a 100-fold improvement with regard to the performance of the sdAb serum fraction, and it is 100-fold better than the IC(50) attained with other antihapten VHHs reported thus far. Despite the modest overall antihapten sdAbs response in llamas, a small subpopulation of high-affinity VHHs is generated that can be isolated by careful design of the selection process.
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Affiliation(s)
- Sofia Tabares-da Rosa
- Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
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Makvandi-Nejad S, Fjällman T, Arbabi-Ghahroudi M, MacKenzie CR, Hall JC. Selection and expression of recombinant single domain antibodies from a hyper-immunized library against the hapten azoxystrobin. J Immunol Methods 2011; 373:8-18. [PMID: 21777591 DOI: 10.1016/j.jim.2011.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 07/04/2011] [Accepted: 07/05/2011] [Indexed: 10/18/2022]
Abstract
Three V(H)Hs against the model hapten, azoxystrobin (MW 403), were isolated from a hyper-immunized phage-displayed V(H)H library. This library was constructed by isolating the V(H)H-coding genes from the lymphocytes collected from a Llama glama that was immunized with azoxystrobin conjugated to bovine serum albumin (BSA). Six rounds of panning were performed against azoxystrobin conjugated to either ovalbumin (OVA) or rabbit serum albumin (RSA) to enrich clones containing V(H)Hs specific to the hapten. After screening 95 clones, three V(H)Hs (A27, A72, and A85) with different amino acid sequences were identified, expressed in soluble format in Escherichia coli HB2151, and purified using nickel-immobilized metal affinity chromatography. Competitive inhibition enzyme-linked immunosorbent assay (CI-ELISA) showed that A27 and A85 were specific to azoxystrobin while A72 was not. The IC(50) values of A27 and A85 V(H)Hs were 7.2 and 2.0μM, respectively. To our knowledge A85 is one of the highest affinity V(H)Hs that has yet been isolated against a hydrophobic hapten such as azoxystrobin.
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de Marco A. Biotechnological applications of recombinant single-domain antibody fragments. Microb Cell Fact 2011; 10:44. [PMID: 21658216 PMCID: PMC3123181 DOI: 10.1186/1475-2859-10-44] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/09/2011] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Single-domain antibody fragments possess structural features, such as a small dimension, an elevated stability, and the singularity of recognizing epitopes non-accessible for conventional antibodies that make them interesting for several research and biotechnological applications. RESULTS The discovery of the single-domain antibody's potentials has stimulated their use in an increasing variety of fields. The rapid accumulation of articles describing new applications and further developments of established approaches has made it, therefore, necessary to update the previous reviews with a new and more complete summary of the topic. CONCLUSIONS Beside the necessary task of updating, this work analyses in detail some applicative aspects of the single-domain antibodies that have been overseen in the past, such as their efficacy in affinity chromatography, as co-crystallization chaperones, protein aggregation controllers, enzyme activity tuners, and the specificities of the unconventional single-domain fragments.
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Affiliation(s)
- Ario de Marco
- University of Nova Gorica (UNG), Vipavska 13, PO Box 301-SI-5000, Rožna Dolina (Nova Gorica), Slovenia.
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49
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Fanning SW, Horn JR. An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop. Protein Sci 2011; 20:1196-207. [PMID: 21557375 DOI: 10.1002/pro.648] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 11/11/2022]
Abstract
Conventional anti-hapten antibodies typically bind low-molecular weight compounds (haptens) in the crevice between the variable heavy and light chains. Conversely, heavy chain-only camelid antibodies, which lack a light chain, must rely entirely on a single variable domain to recognize haptens. While several anti-hapten VHHs have been generated, little is known regarding the underlying structural and thermodynamic basis for hapten recognition. Here, an anti-methotrexate VHH (anti-MTX VHH) was generated using grafting methods whereby the three complementarity determining regions (CDRs) were inserted onto an existing VHH framework. Thermodynamic analysis of the anti-MTX VHH CDR1-3 Graft revealed a micromolar binding affinity, while the crystal structure of the complex revealed a somewhat surprising noncanonical binding site which involved MTX tunneling under the CDR1 loop. Due to the close proximity of MTX to CDR4, a nonhypervariable loop, the CDR4 loop sequence was subsequently introduced into the CDR1-3 graft, which resulted in a dramatic 1000-fold increase in the binding affinity. Crystal structure analysis of both the free and complex anti-MTX CDR1-4 graft revealed CDR4 plays a significant role in both intermolecular contacts and binding site conformation that appear to contribute toward high affinity binding. Additionally, the anti-MTX VHH possessed relatively high specificity for MTX over closely related compounds aminopterin and folate, demonstrating that VHH domains are capable of binding low-molecular weight ligands with high affinity and specificity, despite their reduced interface.
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Affiliation(s)
- Sean W Fanning
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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50
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Rahbarizadeh F, Ahmadvand D, Sharifzadeh Z. Nanobody; an old concept and new vehicle for immunotargeting. Immunol Invest 2011; 40:299-338. [PMID: 21244216 DOI: 10.3109/08820139.2010.542228] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The use of antibodies in cancer therapy has come a long way since the day Paul Ehrlich described the concept and Kohler and Milstein devised the hybridoma technology to bring this theory to reality. The synthesis of murine monoclonal antibodies (mAbs) was the first success in this field, leading to the invention of chimerization, the production of variable fragments (Fv) with the progression to domain antibodies (dAb) and later humanization technologies to maximize the clinical utility of murine mAbs. It was just by chance that dAbs were found to exist in ?heavy chain? immunoglobulins from Camelidae family and cartilaginous fish. These unique antibody fragments interact with antigen by virtue of only one single variable domain, referred to as VHH or nanobody. Several characteristics make nanobody use superior to the abovementioned antibodies. They are non-immunogenic and show high thermal and chemical stability. There are several reports of raising specific nanobodies against enzymes, haptens, pathogens, toxins and tumor markers, which are outlined in this paper. All these characteristics make them strong candidates as targeting agents for cancer therapy.
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Affiliation(s)
- Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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