1
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Sun H, Wei M, Guo A, Zhang C, Wang Y, Huang R, Li X, Zhan J, Wu J, Jiang B. Shrimp hemocyanin elicits a potent humoral response in mammals and is favorable to hapten conjugation. Sci Rep 2024; 14:16771. [PMID: 39039159 PMCID: PMC11263335 DOI: 10.1038/s41598-024-67715-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024] Open
Abstract
Conjugation to a carrier protein is essential to give rise to the antigenicity of hapten. Three carrier proteins e.g. KLH (Keyhole Limpet hemocyanin), BSA (bovine serum albumin), and OVA (Ovalbumin) were used mostly. KLH is advantageous to the others, majorly owing to its strong immunogenicity and limited usage in other biological assays. However, the cost of obtaining Keyhole Limpet is high and the solubility of KLH is not as well as the other carriers, especially after hapten conjugation. Here, we extracted the shrimp hemocyanin (SHC) from Litopenaeus vannamei (L. vannamei), which is a commonly sea product worldwide. The high pure SHC could be acquired by two-step purification, with a production yield of > 1 g proteins (98% pure) per 1 kg shrimp. Compared to KLH, the peptide-SHC conjugates exhibit higher solubility after hapten conjugation. Meanwhile, compared with KLH, SHC induces comparable antibody production efficiency in mammals, with or without conjugation. Furthermore, rabbit polyclonal antibodies or mouse monoclonal antibodies were generated by immunizing SHC-peptide conjugates, and the subsequent antibodies were confirmed to be used in western blot, immunofluorescence and immunohistochemistry. Therefore, we demonstrated that SHC may be used as a substitute for KLH in future antibody and vaccine development.
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Affiliation(s)
- Huiwen Sun
- Shanghai Epizyme BioMedical, Shanghai, China
| | - Moris Wei
- Shanghai Epizyme BioMedical, Shanghai, China
| | - Amber Guo
- Shanghai Epizyme BioMedical, Shanghai, China
| | - Ci Zhang
- Shanghai Epizyme BioMedical, Shanghai, China
| | - Yuefeng Wang
- Shanghai Epizyme BioMedical, Shanghai, China
- Shanghai Yilawo Biotech., Shanghai, China
| | - Renhui Huang
- Shanghai Epizyme BioMedical, Shanghai, China
- Tongling Epizyme BioMedical, Tongling, China
| | - Xiaoxiao Li
- Shanghai Epizyme BioMedical, Shanghai, China
| | | | - Jonny Wu
- Shanghai Epizyme BioMedical, Shanghai, China.
- Tongling Epizyme BioMedical, Tongling, China.
| | - Bruce Jiang
- Shanghai Epizyme BioMedical, Shanghai, China.
- Tongling Epizyme BioMedical, Tongling, China.
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2
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Qin L, Xiao J, Yang H, Liang J, Li L, Wu S, Peng D. Rapid immunoassays for the detection of quinoxalines and their metabolites residues in animal-derived foods: A review. Food Chem 2024; 443:138539. [PMID: 38320375 DOI: 10.1016/j.foodchem.2024.138539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/06/2024] [Accepted: 01/20/2024] [Indexed: 02/08/2024]
Abstract
Quinoxalines are a class of veterinary drugs with antibacterial and growth-promoting functions. They are often widely used to treat and prevent animal diseases and are illegally used as animal growth promoters to increase economic benefits. Quinoxalines could be easily metabolized in animals to various residue markers and remain in animal-derived foods, which would pose a serious threat to human health. Consequently, it is necessary to detect the residues of quinoxalines and their metabolites. This article reviewed and evaluated immunoassays for quinoxalines and their metabolites in animal-derived foods, mainly including enzyme-linked immunosorbent assays, fluorescence immunosorbent assays, immunochromatography, and surface plasmon resonance biosensors. In addition, we deeply explored the design of haptens for quinoxalines and their metabolites and analyzed the effect of haptens on antibody performance. This paper aims to provide guidance and references for their accurate and sensitive detection, thereby ensuring food safety and human public health.
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Affiliation(s)
- Liangni Qin
- State Key Laboratory of Agricultural Microbiology, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaxu Xiao
- State Key Laboratory of Agricultural Microbiology, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongfei Yang
- State Key Laboratory of Agricultural Microbiology, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Jixiang Liang
- State Key Laboratory of Agricultural Microbiology, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Li
- State Key Laboratory of Agricultural Microbiology, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Shixiang Wu
- State Key Laboratory of Agricultural Microbiology, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Dapeng Peng
- State Key Laboratory of Agricultural Microbiology, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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3
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Rezaei S, Sefidbakht Y, Uskoković V. Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design. Brief Bioinform 2021; 22:6313266. [PMID: 34219142 DOI: 10.1093/bib/bbab241] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/23/2021] [Accepted: 06/04/2021] [Indexed: 12/23/2022] Open
Abstract
With the onset of the COVID-19 pandemic, the amount of data on genomic and proteomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stored in various databases has exponentially grown. A large volume of these data has led to the production of equally immense sets of immunological data, which require rigorous computational approaches to sort through and make sense of. Immunoinformatics has emerged in the recent decades as a field capable of offering this approach by bridging experimental and theoretical immunology with state-of-the-art computational tools. Here, we discuss how immunoinformatics can assist in the development of high-performance vaccines and drug discovery needed to curb the spread of SARS-CoV-2. Immunoinformatics can provide a set of computational tools to extract meaningful connections from the large sets of COVID-19 patient data, which can be implemented in the design of effective vaccines. With this in mind, we represent a pipeline to identify the role of immunoinformatics in COVID-19 treatment and vaccine development. In this process, a number of free databases of protein sequences, structures and mutations are introduced, along with docking web servers for assessing the interaction between antibodies and the SARS-CoV-2 spike protein segments as most commonly considered antigens in vaccine design.
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Affiliation(s)
- Shokouh Rezaei
- Protein Research Center at Shahid Beheshti University, Tehran, Iran
| | - Yahya Sefidbakht
- Protein Research Center at Shahid Beheshti University, Tehran, Iran
| | - Vuk Uskoković
- Founder of the biotech startup, TardigradeNano, and formerly a Professor at University of Illinois in Chicago, Chapman University, and University of California in Irvine
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4
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Maselis K, Žekevičiūtė R, Vaitkus A. Refractoriness to drugs in migraine may be the result of developing anti-drug antibodies. Med Hypotheses 2020; 146:110459. [PMID: 33360448 DOI: 10.1016/j.mehy.2020.110459] [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: 10/26/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Migraine is a common neurological disease and is listed second among the most disabling health conditions worldwide. Refractory migraine (RM) is a term used to emphasize the unresponsiveness of migraine to various treatment options, encompassing both episodic refractory and chronic refractory migraine. In this paper we discuss various known and possible mechanisms of pharmacological refractoriness in RM, such as possible involvement of the gut microbiome, the blood-brain barrier, migraine genetics and various mechanisms of pharmacokinetic and pharmacodynamic tolerance. Development of medication-overuse headache as a secondary disorder following migraine is also considered. We argue that the available literature is insufficient to fully explain the mechanisms of refractoriness and we present our hypothesis. HYPOTHESIS Refractoriness to drugs in migraine may be the result of developing anti-drug antibodies. Most migraine drugs are small molecules, which cannot elicit an immune response on their own due to their size. However, such molecules can bind to peptide carriers in their vicinity, greatly increasing their immunogenicity. A small molecule possessing this binding ability is called a hapten. Haptens form hapten-carrier complexes (HCCs), which can evoke powerful immune responses. Immune reactions to HCCs are known to be predominantly 'drug allergies' or type 1 drug hypersensitivity reactions', usually resulting from IgE or non-IgE mediated mast cell degranulation. We argue that the immune reaction to HCCs can take shape in developing neutralizing anti-drug antibodies (ADA) in the form of IgG and IgA class antibodies. Since biological therapeutics, such as various monoclonal antibodies, face the issue of ADA-induced drug tolerance, HCCs, being similar in the sense that they carry peptide antigens, are of sufficient size and may be considerably immunogenic, can be responded to in a similar way by producing neutralizing ADA. Furthermore, we argue that such responses are expected to happen more frequently than is thought, due to IgG and IgA being prevalent antibodies, which utilize their neutralizing capabilities on regular basis. Finally, it is important to consider that neutralization reactions in normal immune responses are typically asymptomatic, with the only clinical expression being progressive drug tolerance. These cases may be overshadowed by the life-threatening cases of drug allergy induced anaphylaxis, possibly leading to neutralization reactions being underrecognized. DISCUSSION This hypothesis aims to stimulate more research regarding drug resistance, and if it receives support from empirical evidence, it may help further elucidate the mechanisms underlying refractory diseases and contribute to the development of more effective treatment of many disorders.
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Affiliation(s)
- K Maselis
- Hospital of Lithuanian, University of Health Sciences Kauno klinikos, Eivenių g. 2, Kaunas, Lithuania.
| | - R Žekevičiūtė
- Hospital of Lithuanian, University of Health Sciences Kauno klinikos, Eivenių g. 2, Kaunas, Lithuania
| | - A Vaitkus
- Lithuanian University of Health Sciences, Eivenių g. 2, Kaunas, Lithuania
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5
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Wen K, Bai Y, Wei Y, Li C, Shen J, Wang Z. Influence of Small Molecular Property on Antibody Response. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10944-10950. [PMID: 32854496 DOI: 10.1021/acs.jafc.0c04333] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antibodies with high titer and affinity to small molecules are critical in the field of vaccines against drugs of abuse, antidotes to toxins, and immunoassays for compounds. However, little is known regarding how properties of small molecules have influence and which molecular descriptors could indicate the degree of the antibody response. On the basis of our previous study, we designed and synthesized two groups of hapten molecules with varied hydrophobicity to investigate the relationship between the properties of the small molecules and the antibody response in terms of titer and affinity. We found that the magnitude of the antibody response was positively correlated with the degree of molecular hydrophobicity and related descriptors. This study provides insight into the immunological characteristics of small molecules themselves and useful clues to produce high-quality antibodies against small molecules.
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Affiliation(s)
- Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China
| | - Yuchen Bai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China
| | - Yujie Wei
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China
| | - Chenglong Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China
| | - Zhanhui Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China
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6
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Fry M. Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:17. [PMID: 32346811 DOI: 10.1007/s40656-020-00310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, POB 9649, 31096, Bat Galim, Haifa, Israel.
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7
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Zhang S, Wu ZY, Zhou K, Luo L, Xu ZL. Development of a competitive indirect ELISA for high-throughput screening of hydrocortisone in cosmetic sample. FOOD AGR IMMUNOL 2019. [DOI: 10.1080/09540105.2019.1608162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Shiwei Zhang
- Shenzhen Academy of Metrology and Quality Inspection, National Nutrition Food Testing Center, Shenzhen, People’s Republic of China
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Zhuo-Yu Wu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Kai Zhou
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Lin Luo
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Zhen-Lin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, People’s Republic of China
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8
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Biological Activity of the Carrier as a Factor in Immunogen Design for Haptens. Molecules 2018; 23:molecules23112977. [PMID: 30441861 PMCID: PMC6278478 DOI: 10.3390/molecules23112977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
Immunoanalytical methods are frequently employed in the detection of hazardous small molecular weight compounds. However, antibody development for these molecules is a challenge, because they are haptens and cannot induce a humoral immune response in experimental animals. Immunogenic forms of haptens are usually prepared by conjugating them to a protein carrier which serves as an immune stimulator. However, the carrier is usually considered merely as a bulk mass, and its biological activity is ignored. Here, we induced an endocytic receptor, transferrin receptor, by selecting its ligand as a carrier protein to enhance antibody production. We conjugated aflatoxin, a potent carcinogenic food contaminant, to transferrin and evaluated its potential to stimulate antibody production with respect to ovalbumin conjugates. Transferrin conjugates induced aflatoxin-specific immune responses in the second immunization, while ovalbumin conjugates reached similar antibody titers after 5 injections. Monoclonal antibodies were successfully developed with mice immunized with either of the conjugates.
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9
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Bucholska J, Minkiewicz P, Darewicz M, Iwaniak A. Databases and Associated Bioinformatic Tools in Studies of Food Allergens, Epitopes and Haptens – a Review. POL J FOOD NUTR SCI 2018. [DOI: 10.1515/pjfns-2017-0022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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10
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Rangnoi K, Choowongkomon K, O'Kennedy R, Rüker F, Yamabhai M. Enhancement and Analysis of Human Antiaflatoxin B1 (AFB1) scFv Antibody-Ligand Interaction Using Chain Shuffling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5713-5722. [PMID: 29781609 DOI: 10.1021/acs.jafc.8b01141] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A human antiaflatoxin B1 (AFB1) scFv antibody (yAFB1-c3), selected from a naı̈ve human phage-displayed scFv library, was used as a template for improving and analysis of antibody-ligand interactions using the chain-shuffling technique. The variable-heavy and variable-light (VH/VL)-shuffled library was constructed from the VH of 25 preselected clones recombined with the VL of yAFB1-c3 and vice versa. Affinity selection from these libraries demonstrated that the VH domain played an important role in the binding of scFv to free AFB1. Therefore, in the next step, VH-shuffled scFv library was constructed from variable-heavy (VH) chain repertoires, amplified from the naı̈ve library, recombined with the variable-light (VL) chain of the clone yAFB1-c3. This library was then used to select a specific scFv antibody against soluble AFB1 by a standard biopanning method. Three clones that showed improved binding properties were isolated. Amino acid sequence analysis indicated that the improved clones have amino acid mutations in framework 1 (FR1) and the complementarity determining region (CDR1) of the VH chain. One clone, designated sAFH-3e3, showed 7.5-fold improvement in sensitivity over the original scFv clone and was selected for molecular binding studies with AFB1. Homology modeling and molecular docking were used to compare the binding of this and the original clones. The results confirmed that VH is more important than VL for AFB1 binding.
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Affiliation(s)
- Kuntalee Rangnoi
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agriculture Technology , Suranaree University of Technology , Nakhon Ratchasima 3000 , Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science , Kasetsart University , 50 Ngam Wong Wan Road, Chatuchak , Bangkok 10900 , Thailand
| | - Richard O'Kennedy
- School of Biotechnology and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Florian Rüker
- Department of Biotechnology , University of National Resource and Life Sciences , Muthgasse 18 , Vienna A-1190 , Austria
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agriculture Technology , Suranaree University of Technology , Nakhon Ratchasima 3000 , Thailand
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11
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Thyparambil AA, Abramyan TM, Bazin I, Guiseppi-Elie A. Site of Tagging Influences the Ochratoxin Recognition by Peptide NFO4: A Molecular Dynamics Study. J Chem Inf Model 2017; 57:2035-2044. [DOI: 10.1021/acs.jcim.7b00312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aby A. Thyparambil
- Center for Bioelectronics, Biosensors and Biochips (C3B), Texas A&M University, College Station, Texas 77843, United States
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Tigran M. Abramyan
- Computational Biophysics & Molecular Design, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7363, United States
| | - Ingrid Bazin
- LGEI,
L’Ecole des Mines d’Ales, Institut Mines Telecom, University of Montpellier, 6 Avenue de Clavieres, 30319 Ales cedex, France
| | - Anthony Guiseppi-Elie
- Center for Bioelectronics, Biosensors and Biochips (C3B), Texas A&M University, College Station, Texas 77843, United States
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, Texas 77843, United States
- LGEI,
L’Ecole des Mines d’Ales, Institut Mines Telecom, University of Montpellier, 6 Avenue de Clavieres, 30319 Ales cedex, France
- ABTECH Scientific, Inc., Biotechnology
Research Park, 800 East Leigh Street, Richmond, Virginia 23219, United States
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12
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Dengl S, Sustmann C, Brinkmann U. Engineered hapten-binding antibody derivatives for modulation of pharmacokinetic properties of small molecules and targeted payload delivery. Immunol Rev 2016; 270:165-77. [PMID: 26864111 PMCID: PMC4755198 DOI: 10.1111/imr.12386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hapten‐binding antibodies have for more than 50 years played a pivotal role in immunology, paving the way to antibody generation (as haptens are very important and robust immunogens), to antibody characterization (as the first structures generated more than 40 years ago were those of hapten binders), and enabled and expanded antibody engineering technologies. The latter field of engineered antibodies evolved over many years and many steps resulting in recombinant humanized or human‐derived antibody derivatives in multiple formats. Today, hapten‐binding antibodies are applied not only as reagents and tools (where they still play an important part) but evolved also to engineered targeting and pretargeting vehicles for disease diagnosis and therapy. Here we describe recent applications of hapten‐binding antibodies and of engineered mono‐ and bispecific hapten‐binding antibody derivatives. We have designed and applied these molecules for the modulation of the pharmacokinetic properties of small compounds or peptides. They are also integrated as additional binding entities into bispecific antibody formats. Here they serve as non‐covalent or covalent coupling modules to haptenylated compounds, to enable targeted payload delivery to disease tissues or cells.
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Affiliation(s)
- Stefan Dengl
- 1Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany
| | - Claudio Sustmann
- 1Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany
| | - Ulrich Brinkmann
- 1Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany
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13
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Production of Polyclonal Antibody and Development of a Competitive Enzyme-Linked Immunosorbent Assay for Benzoic Acid in Foods. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9975-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Khalili S, Jahangiri A, Borna H, Ahmadi Zanoos K, Amani J. Computational vaccinology and epitope vaccine design by immunoinformatics. Acta Microbiol Immunol Hung 2014; 61:285-307. [PMID: 25261943 DOI: 10.1556/amicr.61.2014.3.4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Human immune system includes variety of different cells and molecules correlating with other body systems. These instances complicate the analysis of the system; particularly in postgenomic era by introducing more amount of data, the complexity is increased and necessity of using computational approaches to process and interpret them is more tangible.Immunoinformatics as a subset of bioinformatics is a new approach with variety of tools and databases that facilitate analysis of enormous amount of immunologic data obtained from experimental researches. In addition to directing the insight regarding experiment selections, it helps new thesis design which was not feasible with conventional methods due to the complexity of data. Considering this features immunoinformatics appears to be one of the fields that accelerate the immunological research progression.In this study we discuss advances in genomics and vaccine design and their relevance to the development of effective vaccines furthermore several division of this field and available tools in each item are introduced.
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Affiliation(s)
- Saeed Khalili
- 1 Tarbiat Modares University Department of Medical Biotechnology Tehran Iran
| | - Abolfazl Jahangiri
- 2 Baqiyatallah University of Medical Sciences Applied Microbiology Research Center Tehran Iran
| | - Hojat Borna
- 3 Baqiyatallah Medical Science University Chemical Injuries Research Center Tehran Iran
| | | | - Jafar Amani
- 2 Baqiyatallah University of Medical Sciences Applied Microbiology Research Center Tehran Iran
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15
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Gupta S, Chavan S, Deobagkar DN, Deobagkar DD. Bio/chemoinformatics in India: an outlook. Brief Bioinform 2014; 16:710-31. [PMID: 25159593 DOI: 10.1093/bib/bbu028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/28/2014] [Indexed: 12/25/2022] Open
Abstract
With the advent of significant establishment and development of Internet facilities and computational infrastructure, an overview on bio/chemoinformatics is presented along with its multidisciplinary facts, promises and challenges. The Government of India has paved the way for more profound research in biological field with the use of computational facilities and schemes/projects to collaborate with scientists from different disciplines. Simultaneously, the growth of available biomedical data has provided fresh insight into the nature of redundant and compensatory data. Today, bioinformatics research in India is characterized by a powerful grid computing systems, great variety of biological questions addressed and the close collaborations between scientists and clinicians, with a full spectrum of focuses ranging from database building and methods development to biological discoveries. In fact, this outlook provides a resourceful platform highlighting the funding agencies, institutes and industries working in this direction, which would certainly be of great help to students seeking their career in bioinformatics. Thus, in short, this review highlights the current bio/chemoinformatics trend, educations, status, diverse applicability and demands for further development.
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16
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Davies MN, Guan P, Blythe MJ, Salomon J, Toseland CP, Hattotuwagama C, Walshe V, Doytchinova IA, Flower DR. Using databases and data mining in vaccinology. Expert Opin Drug Discov 2013; 2:19-35. [PMID: 23496035 DOI: 10.1517/17460441.2.1.19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Throughout time functional immunology has accumulated vast amounts of quantitative and qualitative data relevant to the design and discovery of vaccines. Such data includes, but is not limited to, components of the host and pathogen genome (including antigens and virulence factors), T- and B-cell epitopes and other components of the antigen presentation pathway and allergens. In this review the authors discuss a range of databases that archive such data. Built on such information, increasingly sophisticated data mining techniques have developed that create predictive models of utilitarian value. With special reference to epitope data, the authors discuss the strengths and weaknesses of the available techniques and how they can aid computer-aided vaccine design deliver added value for vaccinology.
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Affiliation(s)
- Matthew N Davies
- The Jenner Institute, University of Oxford, Compton, Berkshire, RG20 7NN, UK.
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Aithal A, Sharma A, Joshi S, Raghava GPS, Varshney GC. PolysacDB: a database of microbial polysaccharide antigens and their antibodies. PLoS One 2012; 7:e34613. [PMID: 22509333 PMCID: PMC3324500 DOI: 10.1371/journal.pone.0034613] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 03/02/2012] [Indexed: 11/30/2022] Open
Abstract
Vaccines based on microbial cell surface polysaccharides have long been considered as attractive means to control infectious diseases. To realize this goal, detailed systematic information about the antigenic polysaccharide is necessary. However, only a few databases that provide limited knowledge in this area are available. This paper describes PolysacDB, a manually curated database of antigenic polysaccharides. We collected and compiled comprehensive information from literature and web resources about antigenic polysaccharides of microbial origin. The current version of the database has 1,554 entries of 149 different antigenic polysaccharides from 347 different microbes. Each entry provides comprehensive information about an antigenic polysaccharide, i.e., its origin, function, protocols for its conjugation to carriers, antibodies produced, details of assay systems, specificities of antibodies, proposed epitopes involved and antibody utilities. For convenience to the user, we have integrated web interface for searching, advanced searching and browsing data in database. This database will be useful for researchers working on polysaccharide-based vaccines. It is freely available from the URL: http://crdd.osdd.net/raghava/polysacdb/.
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Affiliation(s)
- Abhijit Aithal
- Cell Biology and Immunology Division, Institute of Microbial Technology, Chandigarh, India
| | - Arun Sharma
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India
| | - Shilpy Joshi
- Cell Biology and Immunology Division, Institute of Microbial Technology, Chandigarh, India
| | - Gajendra P. S. Raghava
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India
- * E-mail: (GPSR); (GCV)
| | - Grish C. Varshney
- Cell Biology and Immunology Division, Institute of Microbial Technology, Chandigarh, India
- * E-mail: (GPSR); (GCV)
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Liu B, Teng D, Yang Y, Wang X, Wang J. Development of a competitive ELISA for the detection of soybean α subunit of β-conglycinin. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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One-Step Detection of Aflatoxin-B1 Using scFv-Alkaline Phosphatase-Fusion Selected from Human Phage Display Antibody Library. Mol Biotechnol 2011; 49:240-9. [DOI: 10.1007/s12033-011-9398-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Ma X, Sun P, He P, Han P, Wang J, Qiao S, Li D. Development of monoclonal antibodies and a competitive ELISA detection method for glycinin, an allergen in soybean. Food Chem 2010. [DOI: 10.1016/j.foodchem.2009.12.045] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B. The immune epitope database 2.0. Nucleic Acids Res 2009; 38:D854-62. [PMID: 19906713 PMCID: PMC2808938 DOI: 10.1093/nar/gkp1004] [Citation(s) in RCA: 475] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Immune Epitope Database (IEDB, www.iedb.org) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes. Epitopes recognized in humans, nonhuman primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. Over the course of 4 years, the data from 180 978 experiments were curated manually from the literature, which covers ∼99% of all publicly available information on peptide epitopes mapped in infectious agents (excluding HIV) and 93% of those mapped in allergens. In addition, data that would otherwise be unavailable to the public from 129 186 experiments were submitted directly by investigators. The curation of epitopes related to autoimmunity is expected to be completed by the end of 2010. The database can be queried by epitope structure, source organism, MHC restriction, assay type or host organism, among other criteria. The database structure, as well as its querying, browsing and reporting interfaces, was completely redesigned for the IEDB 2.0 release, which became publicly available in early 2009.
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Affiliation(s)
- Randi Vita
- La Jolla Institute for Allergy and Immunology, Center For Infectious Disease, Allergy and Asthma Research, 9420 Athena Circle, La Jolla, CA 92037, USA.
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22
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Yang X, Yu X. An introduction to epitope prediction methods and software. Rev Med Virol 2009; 19:77-96. [PMID: 19101924 DOI: 10.1002/rmv.602] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this paper, current prediction methods and algorithms for both T- and B cell epitopes are reviewed, and a comprehensive summary of epitope prediction software and databases currently available online is also provided. This review can offer researchers in this field a sense of direction and insights for future work. However, our main purpose is to introduce clinical and basic biomedical researchers who are not familiar with these biological analysis tools and databases to these online resources and to provide guidance on how to use them effectively.
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Affiliation(s)
- Xingdong Yang
- Department of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, P. R. China
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Lata S, Raghava GPS. PRRDB: a comprehensive database of pattern-recognition receptors and their ligands. BMC Genomics 2008; 9:180. [PMID: 18423032 PMCID: PMC2346480 DOI: 10.1186/1471-2164-9-180] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Accepted: 04/18/2008] [Indexed: 11/23/2022] Open
Abstract
Background Recently in a number of studies, it has been demonstrated that the innate immune system doesn't merely acts as the first line of defense but provides critical signals for the development of specific adaptive immune response. Innate immune system employs a set of receptors called pattern recognition receptors (PRRs) that recognize evolutionarily conserved patterns from pathogens called pathogen associated molecular patterns (PAMPs). In order to assist scientific community, a database PRRDB has been developed that provides extensive information about pattern recognition receptors and their ligands. Results The current version of database contains around 500 patterns recognizing receptors from 77 distinct organisms ranging from insects to human. This includes 177 Toll-like receptors, 124 are Scavenger receptors and 67 are Nucleotide Binding Site-Leucine repeats rich receptors. The database also provides information about 266 ligands that includes carbohydrates, proteins, nucleic acids, glycolipids, glycoproteins, lipopeptides. A number of web tools have been integrated in PRRDB in order to provide following services: i) searching on any field; ii) database browsing; and iii) BLAST search against the pattern-recognition receptors. PRRDB also provides external links to standard databases like Swiss-Prot and Pubmed. Conclusion PRRDB is a unique database of its kind, which provides comprehensive information about innate immunity. This database will be very useful in designing effective adjuvant for subunit vaccine and in understanding role of innate immunity. The database is available from the URL's in the Availabiltiy and requirements section.
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Affiliation(s)
- Sneh Lata
- Institute of Microbial Technology, Sector39A, Chandigarh, India.
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Vivona S, Gardy JL, Ramachandran S, Brinkman FSL, Raghava GPS, Flower DR, Filippini F. Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol 2008; 26:190-200. [PMID: 18291542 DOI: 10.1016/j.tibtech.2007.12.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 12/06/2007] [Accepted: 12/19/2007] [Indexed: 11/18/2022]
Abstract
Genome sequences from many organisms, including humans, have been completed, and high-throughput analyses have produced burgeoning volumes of 'omics' data. Bioinformatics is crucial for the management and analysis of such data and is increasingly used to accelerate progress in a wide variety of large-scale and object-specific functional analyses. Refined algorithms enable biotechnologists to follow 'computer-aided strategies' based on experiments driven by high-confidence predictions. In order to address compound problems, current efforts in immuno-informatics and reverse vaccinology are aimed at developing and tuning integrative approaches and user-friendly, automated bioinformatics environments. This will herald a move to 'computer-aided biotechnology': smart projects in which time-consuming and expensive large-scale experimental approaches are progressively replaced by prediction-driven investigations.
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Affiliation(s)
- Sandro Vivona
- Molecular Biology and Bioinformatics Unit, Department of Biology, University of Padua, Padua, Italy
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Development of a high-throughput enzyme-linked immunosorbent assay for the routine detection of the carcinogen acrylamide in food, via rapid derivatisation pre-analysis. Anal Chim Acta 2008; 608:178-85. [DOI: 10.1016/j.aca.2007.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 12/09/2007] [Accepted: 12/13/2007] [Indexed: 11/19/2022]
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26
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Tang Z, Han L, Xie B, Ung CY, Jiang L, Cao Z, Chen Y. AAIR: antibody antigen information resource. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2007; 178:4705. [PMID: 17404245 DOI: 10.4049/jimmunol.178.8.4705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
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Alvarez-Rueda N, Behar G, Ferré V, Pugnière M, Roquet F, Gastinel L, Jacquot C, Aubry J, Baty D, Barbet J, Birklé S. Generation of llama single-domain antibodies against methotrexate, a prototypical hapten. Mol Immunol 2007; 44:1680-90. [PMID: 17011035 DOI: 10.1016/j.molimm.2006.08.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
Single-domain antibodies specific to methotrexate (MTX) were obtained after immunization of one llama (Llama glama). Specific VHH domains (V-D-J-REGION) were selected by panning from an immune-llama library using phage display technology. The antibody fragments specific to MTX were purified from Escherichia coli (C41 strain) periplasm by immobilized metal affinity chromatography with an expression level of around 10mg/L. A single band around 16,000Da corresponding to VHH fragments was found after analysis by SDS-PAGE and Western blotting, while competition ELISA demonstrated selective binding to soluble MTX. Surface plasmon resonance (SPR) analysis showed that anti-MTX VHH domains had affinities in the nanomolar range (29-515nM) to MTX-serum albumin conjugates. The genes encoding anti-MTX VHH were found by IMGT/V-QUEST to be similar to the previously reported llama and human IGHV germline genes. The V-D and D-J junction rearrangements in the seven anti-MTX CDR3 sequences indicate that they were originated from three distinct progenitor B cells. Our results demonstrate that camelid single-domain antibodies are capable of high affinity binding to low molecular weight hydrosoluble haptens. Furthermore, these anti-MTX VHH give new insights on how the antigen binding repertoire of llama single-domain antibody can provide combining sites to haptens in the absence of a VL. This type of single-domain antibodies offers advantages compared to murine recombinant antibodies in terms of production rate and sequence similarity to the human IGHV3 subgroup genes.
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Affiliation(s)
- Nidia Alvarez-Rueda
- Inserm, Université de Nantes, Nantes Atlantique Universités, U601, Département de Recherche en Cancérologie, 9 quai Moncousu, F-44000 Nantes, France
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Srivastava S, Singh MK, Raghava GPS, Varshney GC. Searching haptens, carrier proteins, and anti-hapten antibodies. Methods Mol Biol 2007; 409:125-139. [PMID: 18449996 DOI: 10.1007/978-1-60327-118-9_8] [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: 05/26/2023]
Abstract
Haptens are small molecules that are usually nonimmunogenic unless coupled to some carrier proteins. The generation of anti-hapten antibodies is important for the development of immunodiagnostics and therapeutics. Recently, our group has developed a database called HaptenDB, which provides comprehensive information about 1,087 haptens. In this chapter, we describe following web tools integrated in HaptenDB: (i) keyword search facility allows search on major fields, (ii) browsing service, to display all haptens, carrier proteins and antibodies, and (iii) structure similarity search, which allows the users to search their structure against hapten structures.
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Günther S, Hempel D, Dunkel M, Rother K, Preissner R. SuperHapten: a comprehensive database for small immunogenic compounds. Nucleic Acids Res 2006; 35:D906-10. [PMID: 17090587 PMCID: PMC1669746 DOI: 10.1093/nar/gkl849] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The immune system protects organisms from foreign proteins, peptide epitopes and a multitude of chemical compounds. Among these, haptens are small molecules, eliciting an immune response when conjugated with carrier molecules. Known haptens are xenobiotics or natural compounds, which can induce a number of autoimmune diseases like contact dermatitis or asthma. Furthermore, haptens are utilized in the development of biosensors, immunomodulators and new vaccines. Although hapten-induced allergies account for 6–10% of all adverse drug effects, the understanding of the correlation between structural and haptenic properties is rather fragmentary. We have developed a manually curated hapten database, SuperHapten, integrating information from literature and web resources. The current version of the database compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. The commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The haptens are classified regarding their origin: pesticides, herbicides, insecticides, drugs, natural compounds, etc. Queries allow identification of haptens and associated antibodies according to functional class, carrier protein, chemical scaffold, composition or structural similarity. SuperHapten is available online at .
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Affiliation(s)
- Stefan Günther
- Institute of Molecular Biology and Bioinformatics, Charité-University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany.
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