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Marino M, Holt MG. AAV Vector-Mediated Antibody Delivery (A-MAD) in the Central Nervous System. Front Neurol 2022; 13:870799. [PMID: 35493843 PMCID: PMC9039256 DOI: 10.3389/fneur.2022.870799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
In the last four decades, monoclonal antibodies and their derivatives have emerged as a powerful class of therapeutics, largely due to their exquisite targeting specificity. Several clinical areas, most notably oncology and autoimmune disorders, have seen the successful introduction of monoclonal-based therapeutics. However, their adoption for treatment of Central Nervous System diseases has been comparatively slow, largely due to issues of efficient delivery resulting from limited permeability of the Blood Brain Barrier. Nevertheless, CNS diseases are becoming increasingly prevalent as societies age, accounting for ~6.5 million fatalities worldwide per year. Therefore, harnessing the full therapeutic potential of monoclonal antibodies (and their derivatives) in this clinical area has become a priority. Adeno-associated virus-based vectors (AAVs) are a potential solution to this problem. Preclinical studies have shown that AAV vector-mediated antibody delivery provides protection against a broad range of peripheral diseases, such as the human immunodeficiency virus (HIV), influenza and malaria. The parallel identification and optimization of AAV vector platforms which cross the Blood Brain Barrier with high efficiency, widely transducing the Central Nervous System and allowing high levels of local transgene production, has now opened a number of interesting scenarios for the development of AAV vector-mediated antibody delivery strategies to target Central Nervous System proteinopathies.
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Affiliation(s)
- Marika Marino
- Laboratory of Glia Biology, VIB-KU Leuven, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Matthew G. Holt
- Laboratory of Glia Biology, VIB-KU Leuven, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, Leuven, Belgium
- Synapse Biology Group, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- *Correspondence: Matthew G. Holt
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102
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V HH Structural Modelling Approaches: A Critical Review. Int J Mol Sci 2022; 23:ijms23073721. [PMID: 35409081 PMCID: PMC8998791 DOI: 10.3390/ijms23073721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/20/2022] Open
Abstract
VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.
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103
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Favorskaya IA, Shcheblyakov DV, Esmagambetov IB, Dolzhikova IV, Alekseeva IA, Korobkova AI, Voronina DV, Ryabova EI, Derkaev AA, Kovyrshina AV, Iliukhina AA, Botikov AG, Voronina OL, Egorova DA, Zubkova OV, Ryzhova NN, Aksenova EI, Kunda MS, Logunov DY, Naroditsky BS, Gintsburg AL. Single-Domain Antibodies Efficiently Neutralize SARS-CoV-2 Variants of Concern. Front Immunol 2022; 13:822159. [PMID: 35281053 PMCID: PMC8907979 DOI: 10.3389/fimmu.2022.822159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/28/2022] [Indexed: 11/21/2022] Open
Abstract
Virus-neutralizing antibodies are one of the few treatment options for COVID-19. The evolution of SARS-CoV-2 virus has led to the emergence of virus variants with reduced sensitivity to some antibody-based therapies. The development of potent antibodies with a broad spectrum of neutralizing activity is urgently needed. Here we isolated a panel of single-domain antibodies that specifically bind to the receptor-binding domain of SARS-CoV-2 S glycoprotein. Three of the selected antibodies exhibiting most robust neutralization potency were used to generate dimeric molecules. We observed that these modifications resulted in up to a 200-fold increase in neutralizing activity. The most potent heterodimeric molecule efficiently neutralized each of SARS-CoV-2 variant of concern, including Alpha, Beta, Gamma, Delta and Omicron variants. This heterodimeric molecule could be a promising drug candidate for a treatment for COVID-19 caused by virus variants of concern.
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Affiliation(s)
- Irina A Favorskaya
- Medical Microbiology Department, Federal State Budget Institution "National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitry V Shcheblyakov
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ilias B Esmagambetov
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Inna V Dolzhikova
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Irina A Alekseeva
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia I Korobkova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Daria V Voronina
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ekaterina I Ryabova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Artem A Derkaev
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anna V Kovyrshina
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anna A Iliukhina
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey G Botikov
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga L Voronina
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Daria A Egorova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga V Zubkova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Natalia N Ryzhova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ekaterina I Aksenova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Marina S Kunda
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Denis Y Logunov
- Medical Microbiology Department, Federal State Budget Institution "National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Boris S Naroditsky
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexandr L Gintsburg
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
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104
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Yu J, Guo Y, Gu Y, Li F, Song H, Nian R, Fan X, Liu W. Targeting and neutralizing human epididymis protein 4 by novel nanobodies to suppress ovarian cancer cells and attenuate cisplatin resistance. Int J Biol Macromol 2022; 199:298-306. [PMID: 35016970 DOI: 10.1016/j.ijbiomac.2022.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 11/05/2022]
Abstract
Human epididymis protein 4 (HE4) is a glycoprotein secreted by epithelial ovarian cancer (EOC) cells and is a novel and specific biomarker for diagnosing and prognosing EOC. Previous studies have shown that overexpression of HE4 is correlated with EOC tumorigenesis and chemoresistance. However, less has been reported regarding the direct effect of the secreted HE4 protein as an autocrine factor in EOC cells. Here, we investigated the molecular mechanism of the secretory form of HE4 on the growth of EOC cells by applying nanobodies with a targeted interaction of free HE4. Three anti-HE4 nanobodies were selected from an immune library by phage display. HE4 secreted by serum-free cultured OVCAR3 cells increased and was effectively neutralized by anti-HE4 nanobodies, which inhibited cell viability. Treatment with the anti-HE4 nanobody 1G8 decreased Bcl-2 expression and increased BAX, cleaved PARP, and p53 levels, resulting in apoptosis of OVCAR3 cells. Moreover, 1G8 significantly improved the cisplatin response of OVCAR3 cells. Our data suggest that secretory HE4 played a novel pro-survival autocrine role and was a target of the anti-HE4 nanobody to improve the therapeutic effects of cisplatin-based chemotherapy.
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Affiliation(s)
- Jianli Yu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Yang Guo
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
| | - Yi Gu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Fei Li
- Shenzhen Innova Nanobodi Co., Ltd., No. 1301 Guanguang Road, Shenzhen 518110, China
| | - Haipeng Song
- Shenzhen Innova Nanobodi Co., Ltd., No. 1301 Guanguang Road, Shenzhen 518110, China
| | - Rui Nian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
| | - Xiying Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China.
| | - Wenshuai Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China.
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105
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X-ray Crystal Structure Analysis of VHH-Protein Antigen Complexes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:513-530. [PMID: 35157291 DOI: 10.1007/978-1-0716-2075-5_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
VHHs are antigen-binding domains cloned from heavy-chain antibodies found in camelids. These proteins have generated considerable interest in a variety of applications as research reagents, crystallization chaperones, and therapeutics. The evolutionary adaptations of VHHs have resulted in biophysical properties and antigen-binding modalities which are distinct from those of conventional antibodies. A detailed molecular analysis of VHH interactions with their cognate protein antigens is valuable for understanding structure-function relationships and for protein engineering. The majority of VHHs bind to folded proteins and thus recognize discontinuous three-dimensional epitopes. While multiple approaches exist for dissecting the interaction between a protein antigen and a VHH, X-ray crystallography remains the highest resolution method available. Here, we provide an updated procedure for determining and analyzing the X-ray structure of a VHH in complex with a protein antigen. We describe the recombinant expression and purification of VHHs and protein antigens, purification and analysis of protein complexes, crystallization, and optimization, X-ray structure determination by molecular replacement, and analysis of the complex.
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106
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Czajka TF, Vance DJ, Davis S, Rudolph MJ, Mantis NJ. Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins. J Biol Chem 2022; 298:101742. [PMID: 35182523 PMCID: PMC8941211 DOI: 10.1016/j.jbc.2022.101742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 12/27/2022] Open
Abstract
During ricin intoxication in mammalian cells, ricin's enzymatic (RTA) and binding (RTB) subunits disassociate in the endoplasmic reticulum. RTA is then translocated into the cytoplasm where, by virtue of its ability to depurinate a conserved residue within the sarcin-ricin loop (SRL) of 28S rRNA, it functions as a ribosome-inactivating protein. It has been proposed that recruitment of RTA to the SRL is facilitated by ribosomal P-stalk proteins, whose C-terminal domains interact with a cavity on RTA normally masked by RTB; however, evidence that this interaction is critical for RTA activity within cells is lacking. Here, we characterized a collection of single-domain antibodies (VHHs) whose epitopes overlap with the P-stalk binding pocket on RTA. The crystal structures of three such VHHs (V9E1, V9F9, and V9B2) in complex with RTA revealed not only occlusion of the ribosomal P-stalk binding pocket but also structural mimicry of C-terminal domain peptides by complementarity-determining region 3. In vitro assays confirmed that these VHHs block RTA-P-stalk peptide interactions and protect ribosomes from depurination. Moreover, when expressed as "intrabodies," these VHHs rendered cells resistant to ricin intoxication. One VHH (V9F6), whose epitope was structurally determined to be immediately adjacent to the P-stalk binding pocket, was unable to neutralize ricin within cells or protect ribosomes from RTA in vitro. These findings are consistent with the recruitment of RTA to the SRL by ribosomal P-stalk proteins as a requisite event in ricin-induced ribosome inactivation.
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Affiliation(s)
- Timothy F Czajka
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - David J Vance
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA; Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Simon Davis
- New York Structural Biology Center, New York, New York, USA
| | | | - Nicholas J Mantis
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA; Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
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107
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Ye J, Guo J, Li T, Tian J, Yu M, Wang X, Majeed U, Song W, Xiao J, Luo Y, Yue T. Phage-based technologies for highly sensitive luminescent detection of foodborne pathogens and microbial toxins: A review. Compr Rev Food Sci Food Saf 2022; 21:1843-1867. [PMID: 35142431 DOI: 10.1111/1541-4337.12908] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 02/05/2023]
Abstract
Foodborne pathogens and microbial toxins are the main causes of foodborne illness. However, trace pathogens and toxins in foods are difficult to detect. Thus, techniques for their rapid and sensitive identification and quantification are urgently needed. Phages can specifically recognize and adhere to certain species of microbes or toxins due to molecular complementation between capsid proteins of phages and receptors on the host cell wall or toxins, and thus they have been successfully developed into a detection platform for pathogens and toxins. This review presents an update on phage-based luminescent detection technologies as well as their working principles and characteristics. Based on phage display techniques of temperate phages, reporter gene detection assays have been designed to sensitively detect trace pathogens by luminous intensity. By the host-specific lytic effects of virulent phages, enzyme-catalyzed chemiluminescent detection technologies for pathogens have been exploited. Notably, these phage-based luminescent detection technologies can discriminate viable versus dead microbes. Further, highly selective and sensitive immune-based assays have been developed to detect trace toxins qualitatively and quantitatively via antibody analogs displayed by phages, such as phage-ELISA (enzyme-linked immunosorbent assay) and phage-IPCR (immuno-polymerase chain reaction). This literature research may lead to novel and innocuous phage-based rapid detection technologies to ensure food safety.
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Affiliation(s)
- Jianming Ye
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jiaqing Guo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Tairan Li
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jiaxin Tian
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Mengxi Yu
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Xiaochen Wang
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Usman Majeed
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Wei Song
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, Ourense, Spain
| | - Yane Luo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China.,Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an, Shaanxi, China.,Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, China
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China.,Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an, Shaanxi, China.,Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, China
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108
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Reichel M, Weitzel V, Klement L, Hoffmann C, Drube J. Suitability of GRK Antibodies for Individual Detection and Quantification of GRK Isoforms in Western Blots. Int J Mol Sci 2022; 23:ijms23031195. [PMID: 35163118 PMCID: PMC8835249 DOI: 10.3390/ijms23031195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are regulated by GPCR kinases (GRKs) which phosphorylate intracellular domains of the active receptor. This results in the recruitment of arrestins, leading to desensitization and internalization of the GPCR. Aside from acting on GPCRs, GRKs regulate a variety of membrane, cytosolic, and nuclear proteins not only via phosphorylation but also by acting as scaffolding partners. GRKs’ versatility is also reflected by their diverse roles in pathological conditions such as cancer, malaria, Parkinson’s-, cardiovascular-, and metabolic disease. Reliable tools to study GRKs are the key to specify their role in complex cellular signaling networks. Thus, we examined the specificity of eight commercially available antibodies targeting the four ubiquitously expressed GRKs (GRK2, GRK3, GRK5, and GRK6) in Western blot analysis. We identified one antibody that did not recognize its antigen, as well as antibodies that showed unspecific signals or cross-reactivity. Hence, we strongly recommend testing any antibody with exogenously expressed proteins to clearly confirm identity of the obtained Western blot results. Utilizing the most-suitable antibodies, we established the Western blot-based, cost-effective simple tag-guided analysis of relative protein abundance (STARPA). This method allows comparison of protein levels obtained by immunoblotting with different antibodies. Furthermore, we applied STARPA to determine GRK protein levels in nine commonly used cell lines, revealing differential isoform expression.
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109
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Wang Y, Zhang C, Wang J, Knopp D. Recent Progress in Rapid Determination of Mycotoxins Based on Emerging Biorecognition Molecules: A Review. Toxins (Basel) 2022; 14:toxins14020073. [PMID: 35202100 PMCID: PMC8874725 DOI: 10.3390/toxins14020073] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/12/2022] Open
Abstract
Mycotoxins are secondary metabolites produced by fungal species, which pose significant risk to humans and livestock. The mycotoxins which are produced from Aspergillus, Penicillium, and Fusarium are considered most important and therefore regulated in food- and feedstuffs. Analyses are predominantly performed by official laboratory methods in centralized labs by expert technicians. There is an urgent demand for new low-cost, easy-to-use, and portable analytical devices for rapid on-site determination. Most significant advances were realized in the field bioanalytical techniques based on molecular recognition. This review aims to discuss recent progress in the generation of native biomolecules and new bioinspired materials towards mycotoxins for the development of reliable bioreceptor-based analytical methods. After brief presentation of basic knowledge regarding characteristics of most important mycotoxins, the generation, benefits, and limitations of present and emerging biorecognition molecules, such as polyclonal (pAb), monoclonal (mAb), recombinant antibodies (rAb), aptamers, short peptides, and molecularly imprinted polymers (MIPs), are discussed. Hereinafter, the use of binders in different areas of application, including sample preparation, microplate- and tube-based assays, lateral flow devices, and biosensors, is highlighted. Special focus, on a global scale, is placed on commercial availability of single receptor molecules, test-kits, and biosensor platforms using multiplexed bead-based suspension assays and planar biochip arrays. Future outlook is given with special emphasis on new challenges, such as increasing use of rAb based on synthetic and naïve antibody libraries to renounce animal immunization, multiple-analyte test-kits and high-throughput multiplexing, and determination of masked mycotoxins, including stereoisomeric degradation products.
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Affiliation(s)
- Yanru Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.W.); (C.Z.)
| | - Cui Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.W.); (C.Z.)
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.W.); (C.Z.)
- Correspondence: (J.W.); (D.K.)
| | - Dietmar Knopp
- Chair for Analytical Chemistry and Water Chemistry, Institute of Hydrochemistry, Technische Universitat München, Elisabeth-Winterhalter-Weg 6, D-81377 München, Germany
- Correspondence: (J.W.); (D.K.)
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110
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Dong S, He K, Guan L, Shi Q, Wu J, Feng J, Yang W, Shi X. Construction and Characterization of a Single-Chain Variable Fragment (scFv) for the Detection of Cry1Ab and Cry1Ac Toxins from the Anti-Cry1Ab Monoclonal Antibody. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-021-02223-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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111
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Matsuzaki Y, Kajiwara K, Aoki W, Ueda M. Production of Single-Domain Antibodies in Pichia pastoris. Methods Mol Biol 2022; 2446:181-203. [PMID: 35157274 DOI: 10.1007/978-1-0716-2075-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-domain antibodies (sdAbs) are binders that consist of a single immunoglobulin domain. SdAbs have gained importance as therapeutics, diagnostic reagents, and research tools. Functional sdAbs are commonly produced in Escherichia coli, which is a simple and widely used host for production of recombinant proteins. However, there are drawbacks of the E. coli expression system, including the potential for misfolded recombinant proteins and pyrogenic contamination with toxic lipopolysaccharides. Pichia pastoris is an alternative host for the production of heterologous proteins because of its high recombinant protein yields and the ability to produce soluble, properly folded proteins without lipopolysaccharide contamination. Here, we describe a method to produce sdAbs in P. pastoris. We present methods for the cloning of sdAb-encoding genes into a P. pastoris expression vector, production and purification of sdAbs, and measurement of sdAb-binding kinetics. Functional sdAbs are easily and routinely obtained using these methods.
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Affiliation(s)
- Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.
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112
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Li D, Peng Q, Huang C, Zang B, Ren J, Ji F, Muyldermans S, Jia L. Cytoplasmic Expression of Nanobodies with Formylglycine Generating Enzyme Tag and Conversion to a Bio-Orthogonal Aldehyde Group. Methods Mol Biol 2022; 2446:357-371. [PMID: 35157283 DOI: 10.1007/978-1-0716-2075-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanobodies (Nbs) can be successfully retrieved following phage, bacterial, yeast, or ribosome display of immune, synthetic, or naïve libraries. However, after panning, multiple individual Nb clones need to be screened and assessed for solubility, antigen specificity, affinity, and potential biological function. Therefore, it is highly desirable to have a convenient expression strategy to obtain sufficient protein for in-depth characterization of the Nbs. The presence of a purification and detection tag, as well as a chemically reactive group to enable simple generation of Nb derivatives, would be of great help in this regard. Here, we provide a general protocol for high yield cytoplasmic expression and purification of formylglycine generating enzyme (FGE)-tagged Nbs. The cysteine within the FGE tag is easily converted to formylglycine by passing the FGE-tag containing Nb over a continuous-flow bio-catalysis system. The aldehyde group within the formylglycine side chain at the C-terminal end of the Nb is suitably located for subsequent bio-orthogonal reactions to fluorescent dyes, biotin, polyethylene glycol, or chromatography resins. We also include methods for production of high yield recombinant FGE, as well as conditions for its immobilization on Sepharose to produce the continuous-flow bio-catalysis system.
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Affiliation(s)
- Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Qiang Peng
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Chungdong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Berlin Zang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China.
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
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113
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Asaadi Y, Jouneghani FF, Janani S, Rahbarizadeh F. A comprehensive comparison between camelid nanobodies and single chain variable fragments. Biomark Res 2021; 9:87. [PMID: 34863296 PMCID: PMC8642758 DOI: 10.1186/s40364-021-00332-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
By the emergence of recombinant DNA technology, many antibody fragments have been developed devoid of undesired properties of natural immunoglobulins. Among them, camelid heavy-chain variable domains (VHHs) and single-chain variable fragments (scFvs) are the most favored ones. While scFv is used widely in various applications, camelid antibodies (VHHs) can serve as an alternative because of their superior chemical and physical properties such as higher solubility, stability, smaller size, and lower production cost. Here, these two counterparts are compared in structure and properties to identify which one is more suitable for each of their various therapeutic, diagnosis, and research applications.
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Affiliation(s)
- Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Fatemeh Fazlollahi Jouneghani
- Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Sara Janani
- Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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114
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Rudenko N, Fursova K, Shepelyakovskaya A, Karatovskaya A, Brovko F. Antibodies as Biosensors' Key Components: State-of-the-Art in Russia 2020-2021. SENSORS 2021; 21:s21227614. [PMID: 34833687 PMCID: PMC8624206 DOI: 10.3390/s21227614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 01/02/2023]
Abstract
The recognition of biomolecules is crucial in key areas such as the timely diagnosis of somatic and infectious diseases, food quality control, and environmental monitoring. This determines the need to develop highly sensitive display devices based on the achievements of modern science and technology, characterized by high selectivity, high speed, low cost, availability, and small size. Such requirements are met by biosensor systems—devices for reagent-free analysis of compounds that consist of a biologically sensitive element (receptor), a transducer, and a working solution. The diversity of biological material and methods for its immobilization on the surface or in the volume of the transducer and the use of nanotechnologies have led to the appearance of an avalanche-like number of different biosensors, which, depending on the type of biologically sensitive element, can be divided into three groups: enzyme, affinity, and cellular/tissue. Affinity biosensors are one of the rapidly developing areas in immunoassay, where the key point is to register the formation of an antigen–antibody complex. This review analyzes the latest work by Russian researchers concerning the production of molecules used in various immunoassay formats as well as new fundamental scientific data obtained as a result of their use.
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115
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Wang X, Li F, Qiu W, Xu B, Li Y, Lian X, Yu H, Zhang Z, Wang J, Li Z, Xue W, Zhu F. SYNBIP: synthetic binding proteins for research, diagnosis and therapy. Nucleic Acids Res 2021; 50:D560-D570. [PMID: 34664670 PMCID: PMC8728148 DOI: 10.1093/nar/gkab926] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/13/2021] [Accepted: 10/14/2021] [Indexed: 12/11/2022] Open
Abstract
The success of protein engineering and design has extensively expanded the protein space, which presents a promising strategy for creating next-generation proteins of diverse functions. Among these proteins, the synthetic binding proteins (SBPs) are smaller, more stable, less immunogenic, and better of tissue penetration than others, which make the SBP-related data attracting extensive interest from worldwide scientists. However, no database has been developed to systematically provide the valuable information of SBPs yet. In this study, a database named ‘Synthetic Binding Proteins for Research, Diagnosis, and Therapy (SYNBIP)’ was thus introduced. This database is unique in (a) comprehensively describing thousands of SBPs from the perspectives of scaffolds, biophysical & functional properties, etc.; (b) panoramically illustrating the binding targets & the broad application of each SBP and (c) enabling a similarity search against the sequences of all SBPs and their binding targets. Since SBP is a human-made protein that has not been found in nature, the discovery of novel SBPs relied heavily on experimental protein engineering and could be greatly facilitated by in-silico studies (such as AI and computational modeling). Thus, the data provided in SYNBIP could lay a solid foundation for the future development of novel SBPs. The SYNBIP is accessible without login requirement at both official (https://idrblab.org/synbip/) and mirror (http://synbip.idrblab.net/) sites.
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Affiliation(s)
- Xiaona Wang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenqi Qiu
- Department of Surgery, HKU-SZH & Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Binbin Xu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yanlin Li
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hongyan Yu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zhao Zhang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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116
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Baum N, Eggers M, Koenigsdorf J, Menzel S, Hambach J, Staehler T, Fliegert R, Kulow F, Adam G, Haag F, Bannas P, Koch-Nolte F. Mouse CD38-Specific Heavy Chain Antibodies Inhibit CD38 GDPR-Cyclase Activity and Mediate Cytotoxicity Against Tumor Cells. Front Immunol 2021; 12:703574. [PMID: 34539634 PMCID: PMC8446682 DOI: 10.3389/fimmu.2021.703574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022] Open
Abstract
CD38 is the major NAD+-hydrolyzing ecto-enzyme in most mammals. As a type II transmembrane protein, CD38 is also a promising target for the immunotherapy of multiple myeloma (MM). Nanobodies are single immunoglobulin variable domains from heavy chain antibodies that naturally occur in camelids. Using phage display technology, we isolated 13 mouse CD38-specific nanobodies from immunized llamas and produced these as recombinant chimeric mouse IgG2a heavy chain antibodies (hcAbs). Sequence analysis assigned these hcAbs to five distinct families that bind to three non-overlapping epitopes of CD38. Members of families 4 and 5 inhibit the GDPR-cyclase activity of CD38. Members of families 2, 4 and 5 effectively induce complement-dependent cytotoxicity against CD38-expressing tumor cell lines, while all families effectively induce antibody dependent cellular cytotoxicity. Our hcAbs present unique tools to assess cytotoxicity mechanisms of CD38-specific hcAbs in vivo against tumor cells and potential off-target effects on normal cells expressing CD38 in syngeneic mouse tumor models, i.e. in a fully immunocompetent background.
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Affiliation(s)
- Natalie Baum
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marie Eggers
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Koenigsdorf
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Radiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Hambach
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Radiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Staehler
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Fliegert
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frederike Kulow
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gerhard Adam
- Department of Radiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Bannas
- Department of Radiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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117
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Mouffak S, Shubbar Q, Saleh E, El-Awady R. Recent advances in management of COVID-19: A review. Biomed Pharmacother 2021; 143:112107. [PMID: 34488083 PMCID: PMC8390390 DOI: 10.1016/j.biopha.2021.112107] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused and is still causing significant mortality and economic consequences all over the globe. As of today, there are three U.S Food and Drug administration (FDA) approved vaccines, Pfizer-BioNTech, Moderna and Janssen COVID-19 vaccine. Also, the antiviral drug remdesivir and two combinations of monoclonal antibodies are authorized for Emergency use (EUA) in certain patients. Furthermore, baricitinib was approved in Japan (April 23, 2021). Despite available vaccines and EUA, pharmacological therapy for the prevention and treatment of COVID-19 is still highly required. There are several ongoing clinical trials investigating the efficacy of clinically available drugs in treating COVID-19. In this study, selected novel pharmacological agents for the possible treatment of COVID-19 will be discussed. Point of discussion will cover mechanism of action, supporting evidence for safety and efficacy and reached stage in development. Drugs were classified into three classes according to the phase of viral life cycle they target. Phase I, the early infective phase, relies on supportive care and symptomatic treatment as needed. In phase II, the pulmonary phase, treatment aims at inhibiting viral entry or replication. Drugs used during this phase are famotidine, monoclonal antibodies, nanobodies, ivermectin, remdesivir, camostat mesylate and other antiviral agents. Finally, phase III, the hyper-inflammatory phase, tocilizumab, dexamethasone, selective serotonin reuptake inhibitors (SSRI), and melatonin are used. The aim of this study is to summarize current findings and suggest gaps in knowledge that can influence future COVID-19 treatment study design.
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Affiliation(s)
- Soraya Mouffak
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Qamar Shubbar
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Ekram Saleh
- Clinical Biochemistry and Molecular Biology Unit, Cancer Biology department, National Cancer Institute, Cairo University, Egypt
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
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118
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Pharmacokinetics of Single Domain Antibodies and Conjugated Nanoparticles Using a Hybrid near Infrared Method. Int J Mol Sci 2021; 22:ijms22168695. [PMID: 34445399 PMCID: PMC8395466 DOI: 10.3390/ijms22168695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
Iron oxide nanoparticles and single domain antibodies from camelids (VHHs) have been increasingly recognized for their potential uses for medical diagnosis and treatment. However, there have been relatively few detailed characterizations of their pharmacokinetics (PK). The aim of this study was to develop imaging methods and pharmacokinetic models to aid the future development of a novel family of brain MRI molecular contrast agents. An efficient near-infrared (NIR) imaging method was established to monitor VHH and VHH conjugated nanoparticle kinetics in mice using a hybrid approach: kinetics in blood were assessed by direct sampling, and kinetics in kidney, liver, and brain were assessed by serial in vivo NIR imaging. These studies were performed under "basal" circumstances in which the VHH constructs and VHH-conjugated nanoparticles do not substantially interact with targets nor cross the blood brain barrier. Using this approach, we constructed a five-compartment PK model that fits the data well for single VHHs, engineered VHH trimers, and iron oxide nanoparticles conjugated to VHH trimers. The establishment of the feasibility of these methods lays a foundation for future PK studies of candidate brain MRI molecular contrast agents.
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119
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Rathinaswamy MK, Fleming KD, Dalwadi U, Pardon E, Harris NJ, Yip CK, Steyaert J, Burke JE. HDX-MS-optimized approach to characterize nanobodies as tools for biochemical and structural studies of class IB phosphoinositide 3-kinases. Structure 2021; 29:1371-1381.e6. [PMID: 34348129 DOI: 10.1016/j.str.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
There is considerable interest in developing antibodies as modulators of signaling pathways. One of the most important signaling pathways in higher eukaryotes is the phosphoinositide 3-kinase (PI3K) pathway, which plays fundamental roles in growth, metabolism, and immunity. The class IB PI3K, PI3Kγ, is a heterodimeric complex composed of a catalytic p110γ subunit bound to a p101 or p84 regulatory subunit. PI3Kγ is a critical component in multiple immune signaling processes and is dependent on activation by Ras and G protein-coupled receptors (GPCRs) to mediate its cellular roles. Here we describe the rapid and efficient characterization of multiple PI3Kγ binding single-chain camelid nanobodies using hydrogen-deuterium exchange (HDX) mass spectrometry (MS) for structural and biochemical studies. We identify nanobodies that stimulated lipid kinase activity, block Ras activation, and specifically inhibited p101-mediated GPCR activation. Overall, our work reveals insight into PI3Kγ regulation and identifies sites that may be exploited for therapeutic development.
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Affiliation(s)
- Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Udit Dalwadi
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada; Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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120
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Kinimi E, Muyldermans S, Vincke C, Odongo S, Kock R, Parida S, Mahapatra M, Misinzo G. Development of Nanobodies Targeting Peste des Petits Ruminants Virus: The Prospect in Disease Diagnosis and Therapy. Animals (Basel) 2021; 11:ani11082206. [PMID: 34438664 PMCID: PMC8388416 DOI: 10.3390/ani11082206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/10/2021] [Accepted: 07/21/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Peste des petits ruminants virus (PPRV) causes a highly devastating disease, peste des petits ruminants (PPR) of sheep and goats, that threatens food security, small ruminant production, and the conservation of wild small ruminants. Current efforts are directed towards the global control and eradication of PPRV, an initiative of the World Organisation for Animal Health and Food and the Agriculture Organisation of the United Nations. A plethora of diagnostic tools for PPR were primarily developed for livestock. New innovative diagnostic tools are needed to detect PPRV in atypical hosts (e.g., Camelidae, Suidae, and Bovinae), in wildlife ecosystems, and in complex field situations. Recent studies confirmed that single-domain antigen binding fragments (nanobodies) derived from heavy-chain-only camelid antibodies have proven to be a powerful tool in diagnostics and therapeutics due to their unique properties, such as small size and strong antigen-binding affinity. Therefore, the main objective of this study was to generate PPRV-reactive nanobodies in order to set a pace for the development of diagnostic and possibly therapeutic nanobodies in the future. Initially, a strategy was developed whereby an alpaca was immunized with PPRV in order to raise an affinity-matured immune response, from which an immune nanobody library was constructed. Following phage display, nine nanobodies that specifically recognise PPRV were identified on enzyme-linked immunosorbent assay. This study has generated PPRV-reactive nanobodies and have significant implications in the development of cost-effective diagnostic tools in context with the planned eradication of PPR in the world. Abstract Peste des petits ruminants virus (PPRV) causes a highly devastating disease, peste des petits ruminants (PPR) of sheep and goats, that threatens food security, small ruminant production, and the conservation of wild small ruminants in many developing countries, especially in Africa. Robust serological and molecular diagnostic tools are available to detect PPRV infection, but they were mainly developed for domestic sheep and goats. The presence of a wide host range for PPRV does present serological diagnostic challenges. New innovative diagnostic tools are needed to detect PPRV in atypical hosts (e.g., Camelidae, Suidae, and Bovinae), in wildlife ecosystems and in complex field situations. Interestingly, single-domain antigen binding fragments (nanobodies) derived from heavy-chain-only camelid antibodies have emerged as a new hope in the development of accurate, rapid, and cost-effective diagnostic tools in veterinary and biomedical fields that are suitable for low-income countries. The main objective of this study was to construct an immune nanobody library to retrieve PPRV-reactive nanobodies that enable the development of diagnostic and therapeutic nanobodies in the future. Here, a strategy was developed whereby an alpaca (Vicugna pacos) was immunized with a live attenuated vaccine strain (PPRV/N/75/1) to raise an affinity-matured immune response in the heavy-chain-only antibody classes. The nanobody gene repertoire was engineered in pMECS-GG phagemid, whereby a ccdB gene (encoding a lethal protein) was substituted by the nanobody gene. An immune nanobody library with approximately sixty-four million independent transformants was constructed, of which 100% contained an insert with the proper size of nanobody gene. Following phage display and biopanning, nine nanobodies that specifically recognise completely inactivated PPRV were identified on enzyme-linked immunosorbent assay. They showed superb potency in rapidly identifying PPRV, which is likely to open a new perspective in the diagnosis and possible treatment of PPR infection.
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Affiliation(s)
- Edson Kinimi
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 25523, Tanzania;
- Department of Veterinary Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3017, Morogoro 25523, Tanzania
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 25523, Tanzania
- Correspondence: (E.K.); (G.M.)
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (S.M.); (C.V.)
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (S.M.); (C.V.)
| | - Steven Odongo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala 7062, Uganda;
| | - Richard Kock
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK;
| | - Satya Parida
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 25523, Tanzania;
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
| | - Mana Mahapatra
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 25523, Tanzania;
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 25523, Tanzania
- Correspondence: (E.K.); (G.M.)
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Xu J, Xu K, Jung S, Conte A, Lieberman J, Muecksch F, Lorenzi JCC, Park S, Schmidt F, Wang Z, Huang Y, Luo Y, Nair MS, Wang P, Schulz JE, Tessarollo L, Bylund T, Chuang GY, Olia AS, Stephens T, Teng IT, Tsybovsky Y, Zhou T, Munster V, Ho DD, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Kwong PD, Casellas R. Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature 2021; 595:278-282. [PMID: 34098567 PMCID: PMC8260353 DOI: 10.1038/s41586-021-03676-z] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/27/2021] [Indexed: 11/08/2022]
Abstract
Since the start of the COVID-19 pandemic, SARS-CoV-2 has caused millions of deaths worldwide. Although a number of vaccines have been deployed, the continual evolution of the receptor-binding domain (RBD) of the virus has challenged their efficacy. In particular, the emerging variants B.1.1.7, B.1.351 and P.1 (first detected in the UK, South Africa and Brazil, respectively) have compromised the efficacy of sera from patients who have recovered from COVID-19 and immunotherapies that have received emergency use authorization1-3. One potential alternative to avert viral escape is the use of camelid VHHs (variable heavy chain domains of heavy chain antibody (also known as nanobodies)), which can recognize epitopes that are often inaccessible to conventional antibodies4. Here, we isolate anti-RBD nanobodies from llamas and from mice that we engineered to produce VHHs cloned from alpacas, dromedaries and Bactrian camels. We identified two groups of highly neutralizing nanobodies. Group 1 circumvents antigenic drift by recognizing an RBD region that is highly conserved in coronaviruses but rarely targeted by human antibodies. Group 2 is almost exclusively focused to the RBD-ACE2 interface and does not neutralize SARS-CoV-2 variants that carry E484K or N501Y substitutions. However, nanobodies in group 2 retain full neutralization activity against these variants when expressed as homotrimers, and-to our knowledge-rival the most potent antibodies against SARS-CoV-2 that have been produced to date. These findings suggest that multivalent nanobodies overcome SARS-CoV-2 mutations through two separate mechanisms: enhanced avidity for the ACE2-binding domain and recognition of conserved epitopes that are largely inaccessible to human antibodies. Therefore, although new SARS-CoV-2 mutants will continue to emerge, nanobodies represent promising tools to prevent COVID-19 mortality when vaccines are compromised.
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MESH Headings
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- CRISPR-Cas Systems
- Camelids, New World/genetics
- Camelids, New World/immunology
- Female
- Gene Editing
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Mutation
- Neutralization Tests
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/genetics
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/isolation & purification
- Somatic Hypermutation, Immunoglobulin/genetics
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Jianliang Xu
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA.
| | - Kai Xu
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Solji Park
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, CCR, NCI, NIH, Frederick, MD, USA
| | | | - Gwo-Yu Chuang
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - I-Ting Teng
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA.
- The NIH Regulome Project, NIH, Bethesda, MD, USA.
- Center for Cancer Research, NCI, NIH, Bethesda, MD, USA.
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122
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Asefy Z, Hoseinnejhad S, Ceferov Z. Nanoparticles approaches in neurodegenerative diseases diagnosis and treatment. Neurol Sci 2021; 42:2653-2660. [PMID: 33846881 DOI: 10.1007/s10072-021-05234-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/07/2021] [Indexed: 01/16/2023]
Abstract
The World Health Organization (WHO) has declared that neurodegenerative diseases will be the biggest health issues of the twenty-first century. Among these, Alzheimer's and Parkinson's diseases can be considered as the most acute incurable neurological diseases. Researchers are studying and developing a new treatment approach that uses nanotechnology to diagnosis and treatment neurodegenerative diseases. This treatment strategy will be used to regress neurodegenerative diseases such as Alzheimer's disease. Alzheimer's disease (AD) is one of the most common forms of reduced brain function, which causes many devastating complications. Current neurodegenerative diseases treatment protocols only help to treat symptoms nevertheless with nanotechnology approaches, can regress nerve cells apoptosis, reduce inflammation, and improve brain drug delivery. In this paper, new nanotechnology methods such as nanobodies, nano-antibodies, and lipid nanoparticles have been investigated. Correspondingly blood-brain barrier drug delivery improvement methods have been suggested.
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Affiliation(s)
- Zahra Asefy
- School of Nursing and Allied Medical Sciences, Maragheh University of Medical Sciences, Maragheh, Iran.
| | - Sirus Hoseinnejhad
- School of Nursing and Allied Medical Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
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123
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Vigano MA, Ell CM, Kustermann MMM, Aguilar G, Matsuda S, Zhao N, Stasevich TJ, Affolter M, Pyrowolakis G. Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster. Development 2021; 148:dev191700. [PMID: 33593816 PMCID: PMC7990863 DOI: 10.1242/dev.191700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 02/09/2021] [Indexed: 01/01/2023]
Abstract
Cellular development and function rely on highly dynamic molecular interactions among proteins distributed in all cell compartments. Analysis of these interactions has been one of the main topics in cellular and developmental research, and has been mostly achieved by the manipulation of proteins of interest (POIs) at the genetic level. Although genetic strategies have significantly contributed to our current understanding, targeting specific interactions of POIs in a time- and space-controlled manner or analysing the role of POIs in dynamic cellular processes, such as cell migration or cell division, would benefit from more-direct approaches. The recent development of specific protein binders, which can be expressed and function intracellularly, along with advancement in synthetic biology, have contributed to the creation of a new toolbox for direct protein manipulations. Here, we have selected a number of short-tag epitopes for which protein binders from different scaffolds have been generated and showed that single copies of these tags allowed efficient POI binding and manipulation in living cells. Using Drosophila, we also find that single short tags can be used for POI manipulation in vivo.
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Affiliation(s)
- M Alessandra Vigano
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Clara-Maria Ell
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Manuela M M Kustermann
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Gustavo Aguilar
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Shinya Matsuda
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - George Pyrowolakis
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
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124
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Njeru FN, Kusolwa PM. Nanobodies: their potential for applications in biotechnology, diagnosis and antiviral properties in Africa; focus on application in agriculture. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1974943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Faith Njeri Njeru
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania
| | - Paul Mbogo Kusolwa
- Department of Crop Science and Horticulture, College of Agriculture, Sokoine University of Agriculture, Morogoro, Tanzania
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