1
|
Xu Y, Zhang F, Mu G, Zhu X. Effect of lactic acid bacteria fermentation on cow milk allergenicity and antigenicity: A review. Compr Rev Food Sci Food Saf 2024; 23:e13257. [PMID: 38284611 DOI: 10.1111/1541-4337.13257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/30/2024]
Abstract
Cow milk is a major allergenic food. The potential prevention and treatment effects of lactic acid bacteria (LAB)-fermented dairy products on allergic symptoms have garnered considerable attention. Cow milk allergy (CMA) is mainly attributed to extracellular and/or cell envelope proteolytic enzymes with hydrolysis specificity. Numerous studies have demonstrated that LAB prevents the risk of allergies by modulating the development and regulation of the host immune system. Specifically, LAB and its effectors can enhance intestinal barrier function and affect immune cells by interfering with humoral and cellular immunity. Fermentation hydrolysis of allergenic epitopes is considered the main mechanism of reducing CMA. This article reviews the linear epitopes of allergens in cow milk and the effect of LAB on these allergens and provides insight into the means of predicting allergenic epitopes by conventional laboratory analysis methods combined with molecular simulation. Although LAB can reduce CMA in several ways, the mechanism of action remains partially clarified. Therefore, this review additionally attempts to summarize the main mechanism of LAB fermentation to provide guidance for establishing an effective preventive and treatment method for CMA and serve as a reference for the screening, research, and application of LAB-based intervention.
Collapse
Affiliation(s)
- Yunpeng Xu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, P. R. China
| | - Feifei Zhang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, P. R. China
| | - Guangqing Mu
- Dalian Key Laboratory of Functional Probiotics, Dalian, Liaoning, P. R. China
| | - Xuemei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, P. R. China
| |
Collapse
|
2
|
Kumar N, Bajiya N, Patiyal S, Raghava GPS. Multi-perspectives and challenges in identifying B-cell epitopes. Protein Sci 2023; 32:e4785. [PMID: 37733481 PMCID: PMC10578127 DOI: 10.1002/pro.4785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/23/2023]
Abstract
The identification of B-cell epitopes (BCEs) in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. Over the past four decades, numerous in silico methods have been developed for predicting BCEs. However, existing reviews have only covered specific aspects, such as the progress in predicting conformational or linear BCEs. Therefore, in this paper, we have undertaken a systematic approach to provide a comprehensive review covering all aspects associated with the identification of BCEs. First, we have covered the experimental techniques developed over the years for identifying linear and conformational epitopes, including the limitations and challenges associated with these techniques. Second, we have briefly described the historical perspectives and resources that maintain experimentally validated information on BCEs. Third, we have extensively reviewed the computational methods developed for predicting conformational BCEs from the structure of the antigen, as well as the methods for predicting conformational epitopes from the sequence. Fourth, we have systematically reviewed the in silico methods developed in the last four decades for predicting linear or continuous BCEs. Finally, we have discussed the overall challenge of identifying continuous or conformational BCEs. In this review, we only listed major computational resources; a complete list with the URL is available from the BCinfo website (https://webs.iiitd.edu.in/raghava/bcinfo/).
Collapse
Affiliation(s)
- Nishant Kumar
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
| | - Nisha Bajiya
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
| | - Sumeet Patiyal
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
| | - Gajendra P. S. Raghava
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
| |
Collapse
|
3
|
Mai Y, Izumi K, Mai S, Nishie W, Ujiie H. Detection of a natural antibody targeting the shed ectodomain of BP180 in mice. J Dermatol Sci 2023; 112:15-22. [PMID: 37550175 DOI: 10.1016/j.jdermsci.2023.07.009] [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: 02/24/2023] [Revised: 06/27/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Pemphigoid diseases are characterized by subepidermal blister formation accompanied by autoantibodies targeting skin component molecules, such as BP180. It is suggested that an epitope-phenotype correlation exists among autoantibodies recognizing BP180. However, it is unclear which regions of BP180 are likely targets for autoantibodies. OBJECTIVE To elucidate the portions of BP180 where antibodies tend to react under the breakdown of immune tolerance. METHODS We immunized mice with full-length mouse BP180 (mBP180) to produce anti-mBP180 antibodies. Using the immunized mice, hybridoma cells were established to produce anti-mBP180 antibodies. We analyzed the characteristics of the anti-mBP180 antibodies that were produced in terms of epitopes, immunoglobulin subclasses, and somatic hypermutations. RESULTS Hybridoma cells derived from immunized mice with full-length mBP180 produced antibodies targeting the intracellular domain (IC) and the shed ectodomain (EC) of mBP180. Using the domain-deleted mBP180 recombinant protein, we revealed that monoclonal anti-mBP180 EC antibodies react to neoepitopes on the 13th collagenous region of cleaved mBP180, which corresponds to the epitopes of linear IgA bullous dermatosis antibodies in human BP180. Furthermore, the subclasses of these antibodies could be distinguished by epitope: The subclass of the anti-mBP180 IC monoclonal antibodies was IgG, whereas that of the anti-mBP180 EC antibodies was IgM. Of note, a clone of these IgM mBP180 EC antibodies was a germline antibody without somatic hypermutation, which is also known as a natural antibody. CONCLUSION These data suggest that mice potentially have natural antibodies targeting the neoepitopes of cleaved mBP180 EC.
Collapse
Affiliation(s)
- Yosuke Mai
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kentaro Izumi
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Shoko Mai
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Wataru Nishie
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hideyuki Ujiie
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| |
Collapse
|
4
|
He J, Li J, Leung K. Dynamic structural analysis-based epitope prediction of Exendin-4 in aqueous solution. Phys Rev E 2023; 108:024403. [PMID: 37723773 DOI: 10.1103/physreve.108.024403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/22/2023] [Indexed: 09/20/2023]
Abstract
The study of epitopes has a broad range of applications in drug discovery, vaccine design, and immunotherapy. In this study, an epitope prediction method was developed based on the dynamic structure of protein antigens. Solvent accessible surface area, charge, and root mean square fluctuation were introduced as the key residue property parameters. The epitope prediction algorithm was established by constructing a three-parameter complex metrics of seven-peptide groups. The method was applied to predict the epitopes of Exendin-4, an effective antidiabetic drug. The epitopes of both the natural and C-terminal amidated forms of Exendin-4 were predicted and compared in their folded and intermediate states. In the folded state, the epitopes of natural Exendin-4 (His1-Phe6 and Asp9-Val19) were found to be nearly identical to the epitopes of C-terminal aminated Exendin-4 (His1-Thr7 and Asp9-Val19). In the intermediate state, however, the epitopes of natural Exendin-4 (His1-Gly4, Phe6 and Lys12-Arg20) covered fewer amino acids than the epitopes of C-terminal aminated Exendin-4 (His1-Gly4, Phe6, Asp9-Val19 and Trp25-Lys27). The comparison with the results from other prediction tools demonstrates the reliability of our predicted epitopes of Exendin-4.
Collapse
Affiliation(s)
- Jianfeng He
- School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Jing Li
- Research and Development Center, Beijing Genetech Pharmaceutical Co., Ltd., Beijing 102200, People's Republic of China
| | - Kingsley Leung
- Uni-Bioscience Pharm Company Limited, Hong Kong, People's Republic of China
| |
Collapse
|
5
|
State of the art in epitope mapping and opportunities in COVID-19. Future Sci OA 2023; 16:FSO832. [PMID: 36897962 PMCID: PMC9987558 DOI: 10.2144/fsoa-2022-0048] [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: 07/29/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
The understanding of any disease calls for studying specific biological structures called epitopes. One important tool recently drawing attention and proving efficiency in both diagnosis and vaccine development is epitope mapping. Several techniques have been developed with the urge to provide precise epitope mapping for use in designing sensitive diagnostic tools and developing rpitope-based vaccines (EBVs) as well as therapeutics. In this review, we will discuss the state of the art in epitope mapping with a special emphasis on accomplishments and opportunities in combating COVID-19. These comprise SARS-CoV-2 variant analysis versus the currently available immune-based diagnostic tools and vaccines, immunological profile-based patient stratification, and finally, exploring novel epitope targets for potential prophylactic, therapeutic or diagnostic agents for COVID-19.
Collapse
|
6
|
Qi Y, Zheng P, Huang G. DeepLBCEPred: A Bi-LSTM and multi-scale CNN-based deep learning method for predicting linear B-cell epitopes. Front Microbiol 2023; 14:1117027. [PMID: 36910218 PMCID: PMC9992402 DOI: 10.3389/fmicb.2023.1117027] [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: 12/06/2022] [Accepted: 01/17/2023] [Indexed: 02/24/2023] Open
Abstract
The epitope is the site where antigens and antibodies interact and is vital to understanding the immune system. Experimental identification of linear B-cell epitopes (BCEs) is expensive, is labor-consuming, and has a low throughput. Although a few computational methods have been proposed to address this challenge, there is still a long way to go for practical applications. We proposed a deep learning method called DeepLBCEPred for predicting linear BCEs, which consists of bi-directional long short-term memory (Bi-LSTM), feed-forward attention, and multi-scale convolutional neural networks (CNNs). We extensively tested the performance of DeepLBCEPred through cross-validation and independent tests on training and two testing datasets. The empirical results showed that the DeepLBCEPred obtained state-of-the-art performance. We also investigated the contribution of different deep learning elements to recognize linear BCEs. In addition, we have developed a user-friendly web application for linear BCEs prediction, which is freely available for all scientific researchers at: http://www.biolscience.cn/DeepLBCEPred/.
Collapse
Affiliation(s)
- Yue Qi
- School of Information Engineering, Shaoyang University, Shaoyang, Hunan, China
| | - Peijie Zheng
- School of Information Engineering, Shaoyang University, Shaoyang, Hunan, China
| | - Guohua Huang
- School of Information Engineering, Shaoyang University, Shaoyang, Hunan, China
| |
Collapse
|
7
|
Zheng D, Liang S, Zhang C. B-Cell Epitope Predictions Using Computational Methods. Methods Mol Biol 2023; 2552:239-254. [PMID: 36346595 DOI: 10.1007/978-1-0716-2609-2_12] [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: 06/16/2023]
Abstract
Identifying protein antigenic epitopes that are recognizable by antibodies is a key step in immunologic research. This type of research has broad medical applications, such as new immunodiagnostic reagent discovery, vaccine design, and antibody design. However, due to the countless possibilities of potential epitopes, the experimental search through trial and error would be too costly and time-consuming to be practical. To facilitate this process and improve its efficiency, computational methods were developed to predict both linear epitopes and discontinuous antigenic epitopes. For linear B-cell epitope prediction, many methods were developed, including PREDITOP, PEOPLE, BEPITOPE, BepiPred, COBEpro, ABCpred, AAP, BCPred, BayesB, BEOracle/BROracle, BEST, LBEEP, DRREP, iBCE-EL, SVMTriP, etc. For the more challenging yet important task of discontinuous epitope prediction, methods were also developed, including CEP, DiscoTope, PEPITO, ElliPro, SEPPA, EPITOPIA, PEASE, EpiPred, SEPIa, EPCES, EPSVR, etc. In this chapter, we will discuss computational methods for B-cell epitope predictions of both linear and discontinuous epitopes. SVMTriP and EPCES/EPCSVR, the most successful among the methods for each type of the predictions, will be used as model methods to detail the standard protocols. For linear epitope prediction, SVMTriP was reported to achieve a sensitivity of 80.1% and a precision of 55.2% with a fivefold cross-validation based on a large dataset, yielding an AUC of 0.702. For discontinuous or conformational B-cell epitope prediction, EPCES and EPCSVR were both benchmarked by a curated independent test dataset in which all antigens had no complex structures with the antibody. The identified epitopes by these methods were later independently validated by various biochemical experiments. For these three model methods, webservers and all datasets are publicly available at http://sysbio.unl.edu/SVMTriP , http://sysbio.unl.edu/EPCES/ , and http://sysbio.unl.edu/EPSVR/ .
Collapse
Affiliation(s)
- Dandan Zheng
- Department of Radiation Oncology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Shide Liang
- Department of Research and Development, Bio-Thera Solutions, Guangzhou, China.
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| |
Collapse
|
8
|
Almalki S, Beigh S, Akhter N, Alharbi RA. In silico epitope-based vaccine design against influenza a neuraminidase protein: Computational analysis established on B- and T-cell epitope predictions. Saudi J Biol Sci 2022; 29:103283. [PMID: 35574284 PMCID: PMC9095894 DOI: 10.1016/j.sjbs.2022.103283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/18/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
Abstract
Objective Influenza A virus belongs to the most studied virus and its mutant initiates epidemic and pandemics outbreaks. Inoculation is the significant foundation to diminish the risk of infection. To prevent an incidence of influenza from the transmission, various practical approaches require more advancement and progress. More efforts and research must take in front to enhance vaccine efficacy. Methods The present research emphasizes the development and expansion of a universal vaccine for the influenza virus. Research focuses on vaccine design with high efficacy. In this study, numerous computational approaches were used, covering a wide range of elements and ideas in bioinformatics methodology. Various B and T-cell epitopic peptides derived from the Neuraminidase protein N1 are recognized by these approaches. With the implementation of numerous obtained databases and bioinformatics tools, the different immune framework methods of the conserved sequences of N1 neuraminidase were analyzed. NCBI databases were employed to retrieve amino acid sequences. The antigenic nature of the neuraminidase sequence was achieved by the VaxiJen server and Kolaskar and Tongaonkar method. After screening of various B and T cell epitopes, one efficient peptide each from B cell epitope and T cell epitopes was assessed for their antigenic determinant vaccine efficacy. Identical two B cell epitopes were recognized from the N1 protein when analyzed using B-cell epitope prediction servers. The detailed examination of amino acid sequences for interpretation of B and T cell epitopes was achieved with the help of the ABCPred and Immune Epitope Database. Results Computational immunology via immunoinformatic study exhibited RPNDKTG as having its high conservancy efficiency and demonstrated as a good antigenic, accessible surface hydrophilic B-cell epitope. Among T cell epitope analysis, YVNISNTNF was selected for being a conserved epitope. T cell epitope was also analyzed for its allergenicity and cytotoxicity evaluation. YVNISNTNF epitope was found to be a non-allergen and not toxic for cells as well. This T-cell epitope with maximum world populace coverages was scrutinized for its association with the HLA-DRB1*0401 molecule. Results from docking simulation analyses showed YVNISNTNF having lower binding energy, the radius of gyration (Rg), RMSD values, and RMSE values which make the protein structure more stable and increase its ability to become an epitopic peptide for influenza virus vaccination. Conclusions We propose that this epitope analysis may be successfully used as a measurement tool for the robustness of an antigen-antibody reaction between mutant strains in the annual design of the influenza vaccine.
Collapse
Key Words
- Antigen-antibody reaction
- Docking simulation
- Epitope prediction
- H1N1, Influenza A
- HA, Hemagglutinin
- HAE, Human airway epithelial
- HCP, Health care personal
- HLA, Human leukocyte antigen
- IC50, Half maximal inhibitory concentration
- IEDB, Immune Epitope Database
- Influenza
- KS, Karplus & Schulz flexibility
- MD, Molecular dynamics
- MMPBSA, Molecular Mechanics Poisson-Boltzmann Surface Area
- NA, Neuraminidase
- RMSD, Root means square deviation
- RMSF, Root mean square fluctuation
- Rg, Radius of gyration
- SARS, Severe acute respiratory syndrome
- Toxicity
- pdm09, Pandemic Disease Mexico 2009
Collapse
Affiliation(s)
- Shaia Almalki
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
| | - Saba Beigh
- Department of Public Health, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
| | - Read A. Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha 65431, Saudi Arabia
| |
Collapse
|
9
|
Tran MH, Schoeder CT, Schey KL, Meiler J. Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook. Front Immunol 2022; 13:859964. [PMID: 35720345 PMCID: PMC9204306 DOI: 10.3389/fimmu.2022.859964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.
Collapse
Affiliation(s)
- Minh H. Tran
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, United States
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Clara T. Schoeder
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
| | - Kevin L. Schey
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Jens Meiler
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
| |
Collapse
|
10
|
Batista AD, Rajpal S, Keitel B, Dietl S, Fresco‐Cala B, Dinc M, Groß R, Sobek H, Münch J, Mizaikoff B. Plastic Antibodies Mimicking the ACE2 Receptor for Selective Binding of SARS-CoV-2 Spike. ADVANCED MATERIALS INTERFACES 2022; 9:2101925. [PMID: 35441074 PMCID: PMC9011513 DOI: 10.1002/admi.202101925] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Molecular imprinting has proven to be a versatile and simple strategy to obtain selective materials also termed "plastic antibodies" for a wide variety of species, i.e., from ions to macromolecules and viruses. However, to the best of the authors' knowledge, the development of epitope-imprinted polymers for selective binding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not reported to date. An epitope from the SARS-CoV-2 spike protein comprising 17 amino acids is used as a template during the imprinting process. The interactions between the epitope template and organosilane monomers used for the polymer synthesis are predicted via molecular docking simulations. The molecularly imprinted polymer presents a 1.8-fold higher selectivity against the target epitope compared to non-imprinted control polymers. Rebinding studies with pseudoviruses containing SARS-CoV-2 spike protein demonstrate the superior selectivity of the molecularly imprinted matrices, which mimic the interactions of angiotensin-converting enzyme 2 receptors from human cells. The obtained results highlight the potential of SARS-CoV-2 molecularly imprinted polymers for a variety of applications including chem/biosensing and antiviral delivery.
Collapse
Affiliation(s)
- Alex D. Batista
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
- Institute of ChemistryFederal University of UberlandiaAv. Joao Naves de Ávila 2121Uberlândia38400‐902Brazil
| | - Soumya Rajpal
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
- Department of Biochemical Engineering and BiotechnologyIndian Institute of Technology DelhiHauz KhasNew Delhi110 016India
| | - Benedikt Keitel
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | - Sandra Dietl
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | - Beatriz Fresco‐Cala
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | | | - Rüdiger Groß
- Institute of Molecular VirologyUlm University Medical CenterMeyerhofstr. 189081UlmGermany
| | - Harald Sobek
- Labor Dr. Merk & Kollegen GmbHBeim Braunland 188416OchsenhausenGermany
| | - Jan Münch
- Institute of Molecular VirologyUlm University Medical CenterMeyerhofstr. 189081UlmGermany
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
- Hahn‐SchickardSedanstraße 1489077UlmGermany
| |
Collapse
|
11
|
Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022; 14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs) are tremendous, the design and discovery of new candidates remain a time and cost-intensive endeavor. In this regard, progress in the generation of data describing antigen binding and developability, computational methodology, and artificial intelligence may pave the way for a new era of in silico on-demand immunotherapeutics design and discovery. Here, we argue that the main necessary machine learning (ML) components for an in silico mAb sequence generator are: understanding of the rules of mAb-antigen binding, capacity to modularly combine mAb design parameters, and algorithms for unconstrained parameter-driven in silico mAb sequence synthesis. We review the current progress toward the realization of these necessary components and discuss the challenges that must be overcome to allow the on-demand ML-based discovery and design of fit-for-purpose mAb therapeutic candidates.
Collapse
Affiliation(s)
- Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Philippe A. Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Eva Smorodina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | | | - Karine Flem-Karlsen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Norway
| | - Talip Zengin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Bioinformatics, Mugla Sitki Kocman University, Turkey
| | | | | | - Jan Terje Andersen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| |
Collapse
|
12
|
Herrera-Bravo J, Farías JG, Contreras FP, Herrera-Belén L, Norambuena JA, Beltrán JF. VirVACPRED: A Web Server for Prediction of Protective Viral Antigens. Int J Pept Res Ther 2021; 28:35. [PMID: 34934411 PMCID: PMC8679566 DOI: 10.1007/s10989-021-10345-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2021] [Indexed: 11/25/2022]
Abstract
Viral antigens are key in the development of vaccines that prevent or eradicate infections caused by these pathogens. Bioinformatics tools are modern alternatives that facilitate the discovery of viral antigens, reducing the costs of experimental assays. We developed a bioinformatics tool called VirVACPRED, which is highly efficient in predicting viral antigens. In this study, we obtained a model based on the gradient boosting classifier, which showed high performance during the training, leave-one-out cross-validation (accuracy = 0.7402, sensitivity = 0.7319, precision = 0.7503, F1 = 0.7251, kappa = 0.4774, Matthews correlation coefficient = 0.4981) and testing (accuracy = 0.8889, sensitivity = 1.0, precision = 0.8276, F1 = 0.9057, kappa = 0.7734, Matthews correlation coefficient = 0.7941). VirVACPRED is a robust tool that can be of great help in the search and proposal of new viral antigens, which can be considered in the development of future vaccines against infections caused by viruses.
Collapse
Affiliation(s)
- Jesús Herrera-Bravo
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Santiago, Chile
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Jorge G. Farías
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Fernanda Parraguez Contreras
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Lisandra Herrera-Belén
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Juan-Alejandro Norambuena
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Program on Natural Resources Sciences, Universidad de La Frontera, Avenida Francisco Salazar, 01145, P.O. Box 54-D, 4780000 Temuco, Chile
| | - Jorge F. Beltrán
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| |
Collapse
|
13
|
Zhang H, Chen P, Ma H, Woińska M, Liu D, Cooper DR, Peng G, Peng Y, Deng L, Minor W, Zheng H. virusMED: an atlas of hotspots of viral proteins. IUCRJ 2021; 8:S2052252521009076. [PMID: 34614039 PMCID: PMC8479994 DOI: 10.1107/s2052252521009076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Metal binding sites, antigen epitopes and drug binding sites are the hotspots in viral proteins that control how viruses interact with their hosts. virusMED (virus Metal binding sites, Epitopes and Drug binding sites) is a rich internet application based on a database of atomic interactions around hotspots in 7041 experimentally determined viral protein structures. 25306 hotspots from 805 virus strains from 75 virus families were characterized, including influenza, HIV-1 and SARS-CoV-2 viruses. Just as Google Maps organizes and annotates points of interest, virusMED presents the positions of individual hotspots on each viral protein and creates an atlas upon which newly characterized functional sites can be placed as they are being discovered. virusMED contains an extensive set of annotation tags about the virus species and strains, viral hosts, viral proteins, metal ions, specific antibodies and FDA-approved drugs, which permits rapid screening of hotspots on viral proteins tailored to a particular research problem. The virusMED portal (https://virusmed.biocloud.top) can serve as a window to a valuable resource for many areas of virus research and play a critical role in the rational design of new preventative and therapeutic agents targeting viral infections.
Collapse
Affiliation(s)
- HuiHui Zhang
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Pei Chen
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Haojie Ma
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- University of Virginia, Charlottesville, VA 22908, USA
| | - Dejian Liu
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | | | - Guo Peng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Yousong Peng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Lei Deng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
- Hunan Provincial Key Laboratory of Medical Virology, People’s Republic of China
| | - Wladek Minor
- University of Virginia, Charlottesville, VA 22908, USA
| | - Heping Zheng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
- Hunan Provincial Key Laboratory of Medical Virology, People’s Republic of China
| |
Collapse
|
14
|
Epitope-Based Immunoinformatic Approach on Heat Shock 70 kDa Protein Complex of Cryptococcus neoformans var. grubii. J Immunol Res 2021; 2021:9921620. [PMID: 34471644 PMCID: PMC8405342 DOI: 10.1155/2021/9921620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Introduction Cryptococcosis is a ubiquitous opportunistic fungal disease caused by Cryptococcus neoformans var. grubii. It has high global morbidity and mortality among HIV patients and non-HIV carriers with 99% and 95%, respectively. Furthermore, the increasing prevalence of undesired toxicity profile of antifungal, multidrug-resistant organisms and the scarcity of FDA-authorized vaccines were the hallmark in the present days. This study was undertaken to design a reliable epitope-based peptide vaccine through targeting highly conserved immunodominant heat shock 70 kDa protein of Cryptococcus neoformans var. grubii that covers a considerable digit of the world population through implementing a computational vaccinology approach. Materials and Methods A total of 38 sequences of Cryptococcus neoformans var. grubii's heat shock 70 kDa protein were retrieved from the NCBI protein database. Different prediction tools were used to analyze the aforementioned protein at the Immune Epitope Database (IEDB) to discriminate the most promising T-cell and B-cell epitopes. The proposed T-cell epitopes were subjected to the population coverage analysis tool to compute the global population's coverage. Finally, the T-cell projected epitopes were ranked based on their binding scores and modes using AutoDock Vina software. Results and Discussion. The epitopes (ANYVQASEK, QSEKPKNVNPVI, SEKPKNVNPVI, and EKPKNVNPVI) had shown very strong binding affinity and immunogenic properties to B-cell. (FTQLVAAYL, YVYDTRGKL) and (FFGGKVLNF, FINAQLVDV, and FDYALVQHF) exhibited a very strong binding affinity to MHC-I and MHC-II, respectively, with high population coverage for each, while FYRQGAFEL has shown promising results in terms of its binding profile to MHC-II and MHC-I alleles and good strength of binding when docked with HLA-C∗12:03. In addition, there is massive global population coverage in the three coverage modes. Accordingly, our in silico vaccine is expected to be the future epitope-based peptide vaccine against Cryptococcus neoformans var. grubii that covers a significant figure of the entire world citizens.
Collapse
|
15
|
Bou Zerdan M, Moussa S, Atoui A, Assi HI. Mechanisms of Immunotoxicity: Stressors and Evaluators. Int J Mol Sci 2021; 22:8242. [PMID: 34361007 PMCID: PMC8348050 DOI: 10.3390/ijms22158242] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022] Open
Abstract
The immune system defends the body against certain tumor cells and against foreign agents such as fungi, parasites, bacteria, and viruses. One of its main roles is to distinguish endogenous components from non-self-components. An unproperly functioning immune system is prone to primary immune deficiencies caused by either primary immune deficiencies such as genetic defects or secondary immune deficiencies such as physical, chemical, and in some instances, psychological stressors. In the manuscript, we will provide a brief overview of the immune system and immunotoxicology. We will also describe the biochemical mechanisms of immunotoxicants and how to evaluate immunotoxicity.
Collapse
Affiliation(s)
- Maroun Bou Zerdan
- Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, 1107 2020 Beirut, Lebanon; (M.B.Z.); (A.A.)
| | - Sara Moussa
- Faculty of Medicine, University of Balamand, 1100 Beirut, Lebanon;
| | - Ali Atoui
- Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, 1107 2020 Beirut, Lebanon; (M.B.Z.); (A.A.)
| | - Hazem I. Assi
- Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, 1107 2020 Beirut, Lebanon; (M.B.Z.); (A.A.)
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Molecular recognition of structurally disordered Pro/Ala-rich sequences (PAS) by antibodies involves an Ala residue at the hot spot of the epitope. J Mol Biol 2021; 433:167113. [PMID: 34161780 DOI: 10.1016/j.jmb.2021.167113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/20/2022]
Abstract
Pro/Ala-rich sequences (PAS) are polypeptides that were developed as a biological alternative to poly-ethylene glycol (PEG) to generate biopharmaceuticals with extended plasma half-life. Like PEG, PAS polypeptides are conformationally disordered and show high solubility in water. Devoid of any charged or prominent hydrophobic side chains, these biosynthetic polymers represent an extreme case of intrinsically disordered proteins. Despite lack of immunogenicity of PAS tags in numerous animal studies we now succeeded in generating monoclonal antibodies (MAbs) against three different PAS versions. To this end, mice were immunized with a PAS#1, P/A#1 or APSA 40mer peptide conjugated to keyhole limpet hemocyanin as highly immunogenic carrier protein. In each case, one MAb with high binding activity and specificity towards a particular PAS motif was obtained. The apparent affinity was strongly dependent on the avidity effect and most pronounced for the bivalent MAb when interacting with a long PAS repeat. X-ray structural analysis of four representative anti-PAS Fab fragments in complex with their cognate PAS epitope peptides revealed interactions dominated by hydrogen bond networks involving the peptide backbone as well as multiple Van der Waals contacts arising from intimate shape complementarity. Surprisingly, Ala, the L-amino acid with the smallest side chain, emerged as a crucial feature for epitope recognition, contributing specific contacts at the center of the paratope in several anti-PAS complexes. Apart from these insights into how antibodies can recognize feature-less peptides without secondary structure, the MAbs characterized in this study offer valuable reagents for the preclinical and clinical development of PASylated biologics.
Collapse
|
18
|
Hou Q, Stringer B, Waury K, Capel H, Haydarlou R, Xue F, Abeln S, Heringa J, Feenstra KA. SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes. Bioinformatics 2021; 37:3421-3427. [PMID: 33974039 PMCID: PMC8136078 DOI: 10.1093/bioinformatics/btab321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/26/2021] [Accepted: 04/26/2021] [Indexed: 11/21/2022] Open
Abstract
Motivation Antibodies play an important role in clinical research and biotechnology, with their specificity determined by the interaction with the antigen’s epitope region, as a special type of protein–protein interaction (PPI) interface. The ubiquitous availability of sequence data, allows us to predict epitopes from sequence in order to focus time-consuming wet-lab experiments toward the most promising epitope regions. Here, we extend our previously developed sequence-based predictors for homodimer and heterodimer PPI interfaces to predict epitope residues that have the potential to bind an antibody. Results We collected and curated a high quality epitope dataset from the SAbDab database. Our generic PPI heterodimer predictor obtained an AUC-ROC of 0.666 when evaluated on the epitope test set. We then trained a random forest model specifically on the epitope dataset, reaching AUC 0.694. Further training on the combined heterodimer and epitope datasets, improves our final predictor to AUC 0.703 on the epitope test set. This is better than the best state-of-the-art sequence-based epitope predictor BepiPred-2.0. On one solved antibody–antigen structure of the COVID19 virus spike receptor binding domain, our predictor reaches AUC 0.778. We added the SeRenDIP-CE Conformational Epitope predictors to our webserver, which is simple to use and only requires a single antigen sequence as input, which will help make the method immediately applicable in a wide range of biomedical and biomolecular research. Availability and implementation Webserver, source code and datasets at www.ibi.vu.nl/programs/serendipwww/. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250002, P. R. China.,National institute of health data science of China, Shandong University, Shandong 250002, P. R. China
| | - Bas Stringer
- IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Katharina Waury
- IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Henriette Capel
- IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Reza Haydarlou
- IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250002, P. R. China.,National institute of health data science of China, Shandong University, Shandong 250002, P. R. China
| | - Sanne Abeln
- IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Jaap Heringa
- IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands.,AIMMS - Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam
| | - K Anton Feenstra
- IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands.,AIMMS - Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam
| |
Collapse
|
19
|
Tilocca B, Britti D, Urbani A, Roncada P. Computational Immune Proteomics Approach to Target COVID-19. J Proteome Res 2020; 19:4233-4241. [PMID: 32914632 PMCID: PMC7640973 DOI: 10.1021/acs.jproteome.0c00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 12/28/2022]
Abstract
Progress of the omics platforms widens their application to diverse fields, including immunology. This enables a deeper level of knowledge and the provision of a huge amount of data for which management and fruitful integration with the past evidence requires a steadily growing computational effort. In light of this, immunoinformatics emerges as a new discipline placed in between the traditional lab-based investigations and the computational analysis of the biological data. Immunoinformatics make use of tailored bioinformatics tools and data repositories to facilitate the analysis of data from a plurality of disciplines and help drive novel research hypotheses and in silico screening investigations in a fast, reliable, and cost-effective manner. Such computational immunoproteomics studies may as well prepare and guide lab-based investigations, representing valuable technology for the investigation of novel pathogens, to tentatively evaluate specificity of diagnostic products, to forecast on potential adverse effects of vaccines and to reduce the use of animal models. The present manuscript provides an overview of the COVID-19 pandemic and reviews the state of the art of the omics technologies employed in fighting SARS-CoV-2 infections. A comprehensive description of the immunoinformatics approaches and its potential role in contrasting COVID-19 pandemics is provided.
Collapse
Affiliation(s)
- Bruno Tilocca
- Department
of Health Sciences, University “Magna
Graecia” of Catanzaro, Catanzaro 88100, Italy
| | - Domenico Britti
- Department
of Health Sciences, University “Magna
Graecia” of Catanzaro, Catanzaro 88100, Italy
| | - Andrea Urbani
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Università Cattolica del
Sacro Cuore, Roma 00168, Italy
- Dipartimento
di Scienze di laboratorio e infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli, Roma 00168, Italy
| | - Paola Roncada
- Department
of Health Sciences, University “Magna
Graecia” of Catanzaro, Catanzaro 88100, Italy
| |
Collapse
|
20
|
Fairén AG, Gómez-Elvira J, Briones C, Prieto-Ballesteros O, Rodríguez-Manfredi JA, López Heredero R, Belenguer T, Moral AG, Moreno-Paz M, Parro V. The Complex Molecules Detector (CMOLD): A Fluidic-Based Instrument Suite to Search for (Bio)chemical Complexity on Mars and Icy Moons. ASTROBIOLOGY 2020; 20:1076-1096. [PMID: 32856927 PMCID: PMC7116096 DOI: 10.1089/ast.2019.2167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Organic chemistry is ubiquitous in the Solar System, and both Mars and a number of icy satellites of the outer Solar System show substantial promise for having hosted or hosting life. Here, we propose a novel astrobiologically focused instrument suite that could be included as scientific payload in future missions to Mars or the icy moons: the Complex Molecules Detector, or CMOLD. CMOLD is devoted to determining different levels of prebiotic/biotic chemical and structural targets following a chemically general approach (i.e., valid for both terrestrial and nonterrestrial life), as well as their compatibility with terrestrial life. CMOLD is based on a microfluidic block that distributes a liquid suspension sample to three instruments by using complementary technologies: (1) novel microscopic techniques for identifying ultrastructures and cell-like morphologies, (2) Raman spectroscopy for detecting universal intramolecular complexity that leads to biochemical functionality, and (3) bioaffinity-based systems (including antibodies and aptamers as capture probes) for finding life-related and nonlife-related molecular structures. We highlight our current developments to make this type of instruments flight-ready for upcoming Mars missions: the Raman spectrometer included in the science payload of the ESAs Rosalind Franklin rover (Raman Laser Spectrometer instrument) to be launched in 2022, and the biomarker detector that was included as payload in the NASA Icebreaker lander mission proposal (SOLID instrument). CMOLD is a robust solution that builds on the combination of three complementary, existing techniques to cover a wide spectrum of targets in the search for (bio)chemical complexity in the Solar System.
Collapse
Affiliation(s)
- Alberto G. Fairén
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca New York, USA
| | - Javier Gómez-Elvira
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | | | | | | | - Raquel López Heredero
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | - Tomás Belenguer
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | - Andoni G. Moral
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | | | - Víctor Parro
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| |
Collapse
|
21
|
Onile OS, Ojo GJ, Oyeyemi BF, Agbowuro GO, Fadahunsi AI. Development of multiepitope subunit protein vaccines against Toxoplasma gondii using an immunoinformatics approach. NAR Genom Bioinform 2020; 2:lqaa048. [PMID: 33575600 PMCID: PMC7671309 DOI: 10.1093/nargab/lqaa048] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/04/2020] [Accepted: 06/21/2020] [Indexed: 12/28/2022] Open
Abstract
Approximately one-third of the world’s human population is estimated to have been exposed to the parasite Toxoplasma gondii. Its prevalence is reportedly high in Ethiopia (74.80%) and Zimbabwe (68.58%), and is 40.40% in Nigeria. The adverse effect of this parasite includes a serious congenital disease in the developing fetus of pregnant women. After several efforts to eliminate the disease, only one licensed vaccine ‘Toxovax’ has been used to avoid congenital infections in sheep. The vaccine has been adjudged expensive coupled with adverse effects and short shelf life. The potential of vaccine to likely revert to virulent strain is a major reason why it has not been found suitable for human use, hence the need for a vaccine that will induce T and B memory cells capable of eliciting longtime immunity against the infection. This study presents immunoinformatics approaches to design a T. gondii-oriented multiepitope subunit vaccine with focus on micronemal proteins for the vaccine construct. The designed vaccine was subjected to antigenicity, immunogenicity, allergenicity and physicochemical parameter analyses. A 657-amino acid multiepitope vaccine was designed with the antigenicity probability of 0.803. The vaccine construct was classified as stable, non-allergenic, and highly immunogenic, thereby indicating the safety of the vaccine construct for human use.
Collapse
Affiliation(s)
- Olugbenga S Onile
- Biotechnology Programme, Department of Biological Sciences, Elizade University, 340211, Ilara-Mokin, Nigeria
| | - Glory J Ojo
- Biotechnology Programme, Department of Biological Sciences, Elizade University, 340211, Ilara-Mokin, Nigeria
| | - Bolaji Fatai Oyeyemi
- Molecular Biology Group, Department of Science Technology, The Federal Polytechnic, 360231, Ado-Ekiti, Ekiti State, Nigeria
| | - Gbenga O Agbowuro
- Biotechnology Programme, Department of Biological Sciences, Elizade University, 340211, Ilara-Mokin, Nigeria
| | - Adeyinka I Fadahunsi
- Biotechnology Programme, Department of Biological Sciences, Elizade University, 340211, Ilara-Mokin, Nigeria
| |
Collapse
|
22
|
Lin Y, Chen Z, Hu C, Chen ZS, Zhang L. Recent progress in antitumor functions of the intracellular antibodies. Drug Discov Today 2020; 25:1109-1120. [DOI: 10.1016/j.drudis.2020.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/10/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023]
|
23
|
Molecular shape as a key source of prebiotic information. J Theor Biol 2020; 499:110316. [PMID: 32387366 DOI: 10.1016/j.jtbi.2020.110316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 01/27/2023]
Abstract
One of the most striking features of a living system is the self-sustaining functional inner organization, which is only possible when a source of internal references is available from which the system is able to self-organize components and processes. Internal references are intrinsically related to biological information, which is typically understood as genetic information. However, the organization in living systems supports a diversity of intricate processes that enable life to endure, adapt and reproduce because of this organization. In a biological context, information refers to a complex relationship between internal architecture and system functionality. Nongenetic processes, such as conformational recognition, are not considered biological information, although they exert important control over cell processes. In this contribution, we discuss the informational nature in the recognition of molecular shape in living systems. Thus, we highlight supramolecular matching as having a theoretical key role in the origin of life. Based on recent data, we demonstrate that the transfer of molecular conformation is a very likely dynamic of prebiotic information, which is closely related to the origin of biological homochirality and biogenic systems. In light of the current hypothesis, we also revisit the central dogma of molecular biology to assess the consistency of the proposal presented here. We conclude that both spatial (molecular shape) and sequential (genetic) information must be represented in this biological paradigm.
Collapse
|
24
|
He B, Dzisoo AM, Derda R, Huang J. Development and Application of Computational Methods in Phage Display Technology. Curr Med Chem 2020; 26:7672-7693. [PMID: 29956612 DOI: 10.2174/0929867325666180629123117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/08/2018] [Accepted: 03/20/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. METHODS We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. RESULTS We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. CONCLUSION The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.
Collapse
Affiliation(s)
- Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China.,School of Medicine, Guizhou University, Guiyang 550025, China
| | - Anthony Mackitz Dzisoo
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| |
Collapse
|
25
|
Abstract
With advancements in sequencing technologies, vast amount of experimental data has accumulated. Due to rapid progress in the development of bioinformatics tools and the accumulation of data, immunoinformatics or computational immunology emerged as a special branch of bioinformatics which utilizes bioinformatics approaches for understanding and interpreting immunological data. One extensively studied aspect of applied immunology involves using available databases and tools for prediction of B- and T-cell epitopes. B and T cells comprise two arms of adaptive immunity.This chapter first reviews the methodology we used for computational identification of B- and T-cell epitopes against enterotoxigenic Escherichia coli (ETEC). Then we discuss other databases of epitopes and analysis tools for T-cell and B-cell epitope prediction and vaccine design. The predicted peptides were analyzed for conservation and population coverage. HLA distribution analysis for predicted epitopes identified efficient MHC binders. Epitopes were further tested using computational docking studies to bind in MHC-I molecule cleft. The predicted epitopes were conserved and covered more than 80% of the world population.
Collapse
MESH Headings
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Computational Biology
- Databases, Protein
- Enterotoxigenic Escherichia coli/genetics
- Enterotoxigenic Escherichia coli/immunology
- Epitope Mapping/methods
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Escherichia coli Vaccines/genetics
- Escherichia coli Vaccines/immunology
- Humans
- Models, Molecular
- Molecular Docking Simulation
Collapse
Affiliation(s)
- Jayashree Ramana
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, HP, India.
| | - Kusum Mehla
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| |
Collapse
|
26
|
EPCES and EPSVR: Prediction of B-Cell Antigenic Epitopes on Protein Surfaces with Conformational Information. Methods Mol Biol 2020; 2131:289-297. [PMID: 32162262 DOI: 10.1007/978-1-0716-0389-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Accurate prediction of discontinuous antigenic epitopes is important for immunologic research and medical applications, but it is not an easy problem. Currently, there are only a few prediction servers available, though discontinuous epitopes constitute the majority of all B-cell antigenic epitopes. In this chapter, we describe two online servers, EPCES and EPSVR, for discontinuous epitope prediction. All methods were benchmarked by a curated independent test set, in which all antigens had no complex structures with the antibody, and their epitopes were identified by various biochemical experiments. The servers and all datasets are available at http://sysbio.unl.edu/EPCES/ and http://sysbio.unl.edu/EPSVR/ .
Collapse
|
27
|
Munteanu CR, Gestal M, Martínez-Acevedo YG, Pedreira N, Pazos A, Dorado J. Improvement of Epitope Prediction Using Peptide Sequence Descriptors and Machine Learning. Int J Mol Sci 2019; 20:ijms20184362. [PMID: 31491969 PMCID: PMC6770149 DOI: 10.3390/ijms20184362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/27/2023] Open
Abstract
In this work, we improved a previous model used for the prediction of proteomes as new B-cell epitopes in vaccine design. The predicted epitope activity of a queried peptide is based on its sequence, a known reference epitope sequence under specific experimental conditions. The peptide sequences were transformed into molecular descriptors of sequence recurrence networks and were mixed under experimental conditions. The new models were generated using 709,100 instances of pair descriptors for query and reference peptide sequences. Using perturbations of the initial descriptors under sequence or assay conditions, 10 transformed features were used as inputs for seven Machine Learning methods. The best model was obtained with random forest classifiers with an Area Under the Receiver Operating Characteristics (AUROC) of 0.981 ± 0.0005 for the external validation series (five-fold cross-validation). The database included information about 83,683 peptides sequences, 1448 epitope organisms, 323 host organisms, 15 types of in vivo processes, 28 experimental techniques, and 505 adjuvant additives. The current model could improve the in silico predictions of epitopes for vaccine design. The script and results are available as a free repository.
Collapse
Affiliation(s)
- Cristian R Munteanu
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, 15071 A Coruña, Spain
- Biomedical Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), 15006 A Coruña, Spain
- Centro de Investigación en Tecnologías de la Información y las Comunicaciones (CITIC), Campus de Elviña s/n, 15071 A Coruña, Spain
| | - Marcos Gestal
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, 15071 A Coruña, Spain.
- Centro de Investigación en Tecnologías de la Información y las Comunicaciones (CITIC), Campus de Elviña s/n, 15071 A Coruña, Spain.
| | - Yunuen G Martínez-Acevedo
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, 15071 A Coruña, Spain
- Unidad Profesional Interdisciplinaria de Biotecnología, National Polytechnic Institute (IPN), Ticoman, 07340 Mexico City, Mexico
| | - Nieves Pedreira
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, 15071 A Coruña, Spain
| | - Alejandro Pazos
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, 15071 A Coruña, Spain
- Biomedical Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Julián Dorado
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, 15071 A Coruña, Spain
- Centro de Investigación en Tecnologías de la Información y las Comunicaciones (CITIC), Campus de Elviña s/n, 15071 A Coruña, Spain
| |
Collapse
|
28
|
Bahrami AA, Payandeh Z, Khalili S, Zakeri A, Bandehpour M. Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein. Int Rev Immunol 2019; 38:307-322. [PMID: 31478759 DOI: 10.1080/08830185.2019.1657426] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Immunoinformatics is a new critical field with several tools and databases that conduct the eyesight of experimental selection and facilitate analysis of the great amount of immunologic data obtained from experimental researches and helps to design and introducing new hypothesis. Given these visages, immunoinformatics seems to be the way that develop and progress the immunological research. Bioinformatics methods and applications are successfully employed in vaccine informatics to assist different sites of the preclinical, clinical, and post-licensure vaccine enterprises. On the other hand, the progression of molecular biology and immunology caused epitope vaccines have become the focus of research on molecular vaccines. Moreover, reverse vaccinology could improve vaccine production and vaccination protocols by in silico prediction of protein-vaccine candidates from genome sequences. B- and T-cell immune epitopes could be predicted by immunoinformatics algorithms and computational methods to improve the vaccine design, protective immunity analysis, assessment of vaccine safety and efficacy, and immunization modeling. This review aims to discuss the power of computational approaches in vaccine design and their relevance to the development of effective vaccines. Furthermore, the various divisions of this field and available tools in each item are introduced and reviewed.
Collapse
Affiliation(s)
- Armina Alagheband Bahrami
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Alireza Zakeri
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mojgan Bandehpour
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
29
|
Ning L, He B, Zhou P, Derda R, Huang J. Molecular Design of Peptide-Fc Fusion Drugs. Curr Drug Metab 2019; 20:203-208. [DOI: 10.2174/1389200219666180821095355] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 01/18/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
Background:Peptide-Fc fusion drugs, also known as peptibodies, are a category of biological therapeutics in which the Fc region of an antibody is genetically fused to a peptide of interest. However, to develop such kind of drugs is laborious and expensive. Rational design is urgently needed.Methods:We summarized the key steps in peptide-Fc fusion technology and stressed the main computational resources, tools, and methods that had been used in the rational design of peptide-Fc fusion drugs. We also raised open questions about the computer-aided molecular design of peptide-Fc.Results:The design of peptibody consists of four steps. First, identify peptide leads from native ligands, biopanning, and computational design or prediction. Second, select the proper Fc region from different classes or subclasses of immunoglobulin. Third, fuse the peptide leads and Fc together properly. At last, evaluate the immunogenicity of the constructs. At each step, there are quite a few useful resources and computational tools.Conclusion:Reviewing the molecular design of peptibody will certainly help make the transition from peptide leads to drugs on the market quicker and cheaper.
Collapse
Affiliation(s)
- Lin Ning
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Alberta, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
30
|
Dingman R, Balu-Iyer SV. Immunogenicity of Protein Pharmaceuticals. J Pharm Sci 2019; 108:1637-1654. [PMID: 30599169 PMCID: PMC6720129 DOI: 10.1016/j.xphs.2018.12.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023]
Abstract
Protein therapeutics have drastically changed the landscape of treatment for many diseases by providing a regimen that is highly specific and lacks many off-target toxicities. The clinical utility of many therapeutic proteins has been undermined by the potential development of unwanted immune responses against the protein, limiting their efficacy and negatively impacting its safety profile. This review attempts to provide an overview of immunogenicity of therapeutic proteins, including immune mechanisms and factors influencing immunogenicity, impact of immunogenicity, preclinical screening methods, and strategies to mitigate immunogenicity.
Collapse
Affiliation(s)
- Robert Dingman
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, New York 14214
| | - Sathy V Balu-Iyer
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, New York 14214.
| |
Collapse
|
31
|
Alfaleh MA, Arora N, Yeh M, de Bakker CJ, Howard CB, Macpherson P, Allavena RE, Chen X, Harkness L, Mahler SM, Jones ML. Canine CD117-Specific Antibodies with Diverse Binding Properties Isolated from a Phage Display Library Using Cell-Based Biopanning. Antibodies (Basel) 2019; 8:E15. [PMID: 31544821 PMCID: PMC6640692 DOI: 10.3390/antib8010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/28/2018] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
CD117 (c-Kit) is a tyrosine kinase receptor that is overexpressed in multiple dog tumors. There is 100% homology between the juxtamembrane domain of human and canine CD117, and many cancer-causing mutations occur in this region in both species. Thus, CD117 is an important target for cancer treatment in dogs and for comparative oncology studies. Currently, there is no monoclonal antibody (mAb) specifically designed to target the exposed region of canine CD117, although there exist some with species cross-reactivity. We panned a naïve phage display library to isolate antibodies against recombinant CD117 on whole cells. Several mAbs were isolated and were shown to bind recombinant canine CD117 at low- to sub-nanomolar affinity. Additionally, binding to native canine CD117 was confirmed by immunohistochemistry and by flow cytometry. Competitive binding assays also identified mAbs that competed with the CD117 receptor-specific ligand, the stem cell factor (SCF). These results show the ability of our cell-based biopanning strategy to isolate a panel of antibodies that have varied characteristics when used in different binding assays. These in vitro/ex vivo assessments suggest that some of the isolated mAbs might be promising candidates for targeting overexpressed CD117 in canine cancers for different useful applications.
Collapse
Affiliation(s)
- Mohamed A Alfaleh
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
- Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center (KFMRC), King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Neetika Arora
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Michael Yeh
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Christopher J de Bakker
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD 4072, Australia.
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Philip Macpherson
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia.
| | - Rachel E Allavena
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia.
| | - Xiaoli Chen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Linda Harkness
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
32
|
Guo C, Zhang H, Xie X, Liu Y, Sun L, Li H, Yu P, Hu H, Sun J, Li Y, Feng Q, Zhao X, Liang D, Wang Z, Hu J. H1N1 influenza virus epitopes classified by monoclonal antibodies. Exp Ther Med 2018; 16:2001-2007. [PMID: 30186431 PMCID: PMC6122413 DOI: 10.3892/etm.2018.6429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 06/22/2018] [Indexed: 12/26/2022] Open
Abstract
Epitopes serve an important role in influenza infection. It may be useful to screen universal influenza virus vaccines, analyzing the epitopes of multiple subtypes of the hemagglutinin (HA) protein. A total of 40 monoclonal antibodies (mAbs) previously obtained from flu virus HA antigens (development and characterization of 40 mAbs generated using H1N1 influenza virus split vaccines were previously published) were used to detect and classify mAbs into distinct flu virus sub-categories using the ELISA method. Following this, the common continuous amino acid sequences were identified by multiple sequence alignment analysis with the GenBank database and DNAMAN software, for use in predicting the epitopes of the HA protein. Synthesized peptides of these common sequences were prepared, and used to verify and determine the predicted linear epitopes through localization and distribution analyses. With these methods, nine HA linear epitopes distributed among different strains of influenza virus were identified, which included three from influenza A, four from 2009 H1N1 and seasonal influenza, and two from H1. The present study showed that considering a combination of the antigen-antibody reaction specificity, variation in the influenza virus HA protein and linear epitopes may present a useful approach for designing effective multi-epitope vaccines. Furthermore, the study aimed to clarify the cause and pathogenic mechanism of influenza virus HA-induced flu, and presents a novel idea for identifying the epitopes of other pathogenic microorganisms.
Collapse
Affiliation(s)
- Chunyan Guo
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Haixiang Zhang
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Xin Xie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Yang Liu
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Lijun Sun
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Huijin Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi 710021, P.R. China
| | - Pengbo Yu
- Center of Shaanxi Provincial Disease Control and Prevention, Institute of Viral Diseases, Xi'an, Shaanxi 710052, P.R. China
| | - Hanyu Hu
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Jingying Sun
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Yuan Li
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Qing Feng
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Xiangrong Zhao
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Daoyan Liang
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Zhen Wang
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Jun Hu
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| |
Collapse
|
33
|
Parvizpour S, Razmara J, Omidi Y. Breast cancer vaccination comes to age: impacts of bioinformatics. ACTA ACUST UNITED AC 2018; 8:223-235. [PMID: 30211082 PMCID: PMC6128970 DOI: 10.15171/bi.2018.25] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/01/2023]
Abstract
![]()
Introduction: Breast cancer, as one of the major causes of cancer death among women, is the central focus of this study. The recent advances in the development and application of computational tools and bioinformatics in the field of immunotherapy of malignancies such as breast cancer have emerged the new dominion of immunoinformatics, and therefore, next generation of immunomedicines .
Methods: Having reviewed the most recent works on the applications of computational tools, we provide comprehensive insights into the breast cancer incidence and its leading causes as well as immunotherapy approaches and the future trends. Furthermore, we discuss the impacts of bioinformatics on different stages of vaccine design for the breast cancer, which can be used to produce much more efficient vaccines through a rationalized time- and cost-effective in silico approaches prior to conducting costly experiments.
Results: The tools can be significantly used for designing the immune system-modulating drugs and vaccines based on in silico approaches prior to in vitro and in vivo experimental evaluations. Application of immunoinformatics in the cancer immunotherapy has shown its success in the pre-clinical models. This success returns back to the impacts of several powerful computational approaches developed during the last decade.
Conclusion: Despite the invention of a number of vaccines for the cancer immunotherapy, more computational and clinical trials are required to design much more efficient vaccines against various malignancies, including breast cancer.
Collapse
Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
34
|
In silico methods for design of biological therapeutics. Methods 2017; 131:33-65. [PMID: 28958951 DOI: 10.1016/j.ymeth.2017.09.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/21/2017] [Accepted: 09/23/2017] [Indexed: 12/18/2022] Open
Abstract
It has been twenty years since the first rationally designed small molecule drug was introduced into the market. Since then, we have progressed from designing small molecules to designing biotherapeutics. This class of therapeutics includes designed proteins, peptides and nucleic acids that could more effectively combat drug resistance and even act in cases where the disease is caused because of a molecular deficiency. Computational methods are crucial in this design exercise and this review discusses the various elements of designing biotherapeutic proteins and peptides. Many of the techniques discussed here, such as the deterministic and stochastic design methods, are generally used in protein design. We have devoted special attention to the design of antibodies and vaccines. In addition to the methods for designing these molecules, we have included a comprehensive list of all biotherapeutics approved for clinical use. Also included is an overview of methods that predict the binding affinity, cell penetration ability, half-life, solubility, immunogenicity and toxicity of the designed therapeutics. Biotherapeutics are only going to grow in clinical importance and are set to herald a new generation of disease management and cure.
Collapse
|
35
|
Schaefer KA, Toral MA, Velez G, Cox AJ, Baker SA, Borcherding NC, Colgan DF, Bondada V, Mashburn CB, Yu CG, Geddes JW, Tsang SH, Bassuk AG, Mahajan VB. Calpain-5 Expression in the Retina Localizes to Photoreceptor Synapses. Invest Ophthalmol Vis Sci 2017; 57:2509-21. [PMID: 27152965 PMCID: PMC4868102 DOI: 10.1167/iovs.15-18680] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose We characterize calpain-5 (CAPN5) expression in retinal and neuronal subcellular compartments. Methods CAPN5 gene variants were classified using the exome variant server, and RNA-sequencing was used to compare expression of CAPN5 mRNA in the mouse and human retina and in retinoblastoma cells. Expression of CAPN5 protein was ascertained in humans and mice in silico, in mouse retina by immunohistochemistry, and in neuronal cancer cell lines and fractionated central nervous system tissue extracts by Western analysis with eight antibodies targeting different CAPN5 regions. Results Most CAPN5 genetic variation occurs outside its protease core; and searches of cancer and epilepsy/autism genetic databases found no variants similar to hyperactivating retinal disease alleles. The mouse retina expressed one transcript for CAPN5 plus those of nine other calpains, similar to the human retina. In Y79 retinoblastoma cells, the level of CAPN5 transcript was very low. Immunohistochemistry detected CAPN5 expression in the inner and outer nuclear layers and at synapses in the outer plexiform layer. Western analysis of fractionated retinal extracts confirmed CAPN5 synapse localization. Western blots of fractionated brain neuronal extracts revealed distinct subcellular patterns and the potential presence of autoproteolytic CAPN5 domains. Conclusions CAPN5 is moderately expressed in the retina and, despite higher expression in other tissues, hyperactive disease mutants of CAPN5 only manifest as eye disease. At the cellular level, CAPN5 is expressed in several different functional compartments. CAPN5 localization at the photoreceptor synapse and with mitochondria explains the neural circuitry phenotype in human CAPN5 disease alleles.
Collapse
Affiliation(s)
- Kellie A Schaefer
- Omics Laboratory, University of Iowa, Iowa City, Iowa, United States 2Department of Ophthalmology & Visual Sciences, University of Iowa, Iowa City, Iowa, United States
| | - Marcus A Toral
- Omics Laboratory, University of Iowa, Iowa City, Iowa, United States 2Department of Ophthalmology & Visual Sciences, University of Iowa, Iowa City, Iowa, United States 3Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, United States
| | - Gabriel Velez
- Omics Laboratory, University of Iowa, Iowa City, Iowa, United States 2Department of Ophthalmology & Visual Sciences, University of Iowa, Iowa City, Iowa, United States 3Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, United States
| | - Allison J Cox
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States
| | - Sheila A Baker
- Department of Ophthalmology & Visual Sciences, University of Iowa, Iowa City, Iowa, United States 5Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States
| | - Nicholas C Borcherding
- Omics Laboratory, University of Iowa, Iowa City, Iowa, United States 3Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, United States
| | - Diana F Colgan
- Omics Laboratory, University of Iowa, Iowa City, Iowa, United States 2Department of Ophthalmology & Visual Sciences, University of Iowa, Iowa City, Iowa, United States
| | - Vimala Bondada
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, United States
| | - Charles B Mashburn
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, United States
| | - Chen-Guang Yu
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, United States
| | - James W Geddes
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, United States
| | - Stephen H Tsang
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, New York, United States
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States 9Neurology, University of Iowa, Iowa City, Iowa, United States
| | - Vinit B Mahajan
- Omics Laboratory, University of Iowa, Iowa City, Iowa, United States 2Department of Ophthalmology & Visual Sciences, University of Iowa, Iowa City, Iowa, United States
| |
Collapse
|
36
|
Li J, Wei H, Krystek SR, Bond D, Brender TM, Cohen D, Feiner J, Hamacher N, Harshman J, Huang RYC, Julien SH, Lin Z, Moore K, Mueller L, Noriega C, Sejwal P, Sheppard P, Stevens B, Chen G, Tymiak AA, Gross ML, Schneeweis LA. Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave Mutagenesis. Anal Chem 2017; 89:2250-2258. [PMID: 28193005 PMCID: PMC5347259 DOI: 10.1021/acs.analchem.6b03058] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics. Five peptide regions on IL-23 with reduced backbone amide solvent accessibility upon antibody binding were identified by HDX-MS, and five different peptides over the same three regions were identified by FPOP. In addition, FPOP analysis at the residue level reveals potentially key interacting residues. Mutants with 3-5 residues changed to alanine have no measurable differences from wild-type IL-23 except for binding of and signaling blockade by the 7B7 anti-IL-23 antibody. The M5 IL-23 mutant differs from wild-type by five alanine substitutions and represents the dominant energetic epitope of 7B7. M5 shows a dramatic decrease in binding to BMS-986010 (which contains the 7B7 Fab, where Fab is fragment antigen-binding region of an antibody), yet it maintains functional activity, binding to p40 and p19 specific reagents, and maintains biophysical properties similar to wild-type IL-23 (monomeric state, thermal stability, and secondary structural features).
Collapse
Affiliation(s)
- Jing Li
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130-4889, USA
| | - Hui Wei
- Biologics Development, Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534
| | - Stanley R. Krystek
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Derek Bond
- Process Development, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Ty M. Brender
- Discovery Biology, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Daniel Cohen
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Jena Feiner
- Applied Genomics, Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534
| | - Nels Hamacher
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Johanna Harshman
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Richard Y.-C. Huang
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Susan H. Julien
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Zheng Lin
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Kristina Moore
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Luciano Mueller
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Claire Noriega
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Preeti Sejwal
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Paul Sheppard
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Brenda Stevens
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130-4889, USA
| | - Lumelle A. Schneeweis
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| |
Collapse
|
37
|
Dalkas GA, Rooman M. SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. BMC Bioinformatics 2017; 18:95. [PMID: 28183272 PMCID: PMC5301386 DOI: 10.1186/s12859-017-1528-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/06/2017] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The identification of immunogenic regions on the surface of antigens, which are able to be recognized by antibodies and to trigger an immune response, is a major challenge for the design of new and effective vaccines. The prediction of such regions through computational immunology techniques is a challenging goal, which will ultimately lead to a drastic limitation of the experimental tests required to validate their efficiency. However, current methods are far from being sufficiently reliable and/or applicable on a large scale. RESULTS We developed SEPIa, a B-cell epitope predictor from the protein sequence, which is sufficiently fast to be applicable on a large scale. The originality of SEPIa lies in the combination of two classifiers, a naïve Bayesian and a random forest classifier, through a voting algorithm that exploits the advantages of both. It is based on 13 sequence-based features, whose values in a 9-residue sequence window are compiled to predict the epitope/non-epitope state of the central residue. The features are related to the type of amino acid, its conservation in homologous proteins, and its tendency of being exposed to the solvent, soluble, flexible, and disordered. The highest signal is obtained from statistical amino acid preferences, but all 13 features contribute non-negligibly in the predictor. SEPIa's average prediction accuracy is limited, with an AUC score (area under the receiver operating characteristic curve) that reaches 0.65 both in 10-fold cross-validation and on an independent test set. It is nevertheless slightly higher than that of other methods evaluated on the same test set. CONCLUSIONS SEPIa was applied to a test protein whose epitopes are known, human β2 adrenergic G-protein-coupled receptor, with promising results. Although the actual AUC score is rather low, many of the predicted epitopes cluster together and overlap the experimental epitope region. The reasons underlying the limitations of SEPIa and of all other B-cell epitope predictors are discussed.
Collapse
Affiliation(s)
- Georgios A. Dalkas
- BioModeling, BioInformatics & BioProcesses (3BIO), Université Libre de Bruxelles (ULB), CP 165/61, 50 Roosevelt Ave, 1050 Brussels, Belgium
- Present address: Institute of Mechanical, Process & Energy Engineering, Heriot-Watt University, Edinburgh, EH14 4AS UK
| | - Marianne Rooman
- BioModeling, BioInformatics & BioProcesses (3BIO), Université Libre de Bruxelles (ULB), CP 165/61, 50 Roosevelt Ave, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, CP 263, Triumph Bld, 1050 Brussels, Belgium
| |
Collapse
|
38
|
Heinson AI, Gunawardana Y, Moesker B, Hume CCD, Vataga E, Hall Y, Stylianou E, McShane H, Williams A, Niranjan M, Woelk CH. Enhancing the Biological Relevance of Machine Learning Classifiers for Reverse Vaccinology. Int J Mol Sci 2017; 18:ijms18020312. [PMID: 28157153 PMCID: PMC5343848 DOI: 10.3390/ijms18020312] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/17/2017] [Indexed: 12/11/2022] Open
Abstract
Reverse vaccinology (RV) is a bioinformatics approach that can predict antigens with protective potential from the protein coding genomes of bacterial pathogens for subunit vaccine design. RV has become firmly established following the development of the BEXSERO® vaccine against Neisseria meningitidis serogroup B. RV studies have begun to incorporate machine learning (ML) techniques to distinguish bacterial protective antigens (BPAs) from non-BPAs. This research contributes significantly to the RV field by using permutation analysis to demonstrate that a signal for protective antigens can be curated from published data. Furthermore, the effects of the following on an ML approach to RV were also assessed: nested cross-validation, balancing selection of non-BPAs for subcellular localization, increasing the training data, and incorporating greater numbers of protein annotation tools for feature generation. These enhancements yielded a support vector machine (SVM) classifier that could discriminate BPAs (n = 200) from non-BPAs (n = 200) with an area under the curve (AUC) of 0.787. In addition, hierarchical clustering of BPAs revealed that intracellular BPAs clustered separately from extracellular BPAs. However, no immediate benefit was derived when training SVM classifiers on data sets exclusively containing intra- or extracellular BPAs. In conclusion, this work demonstrates that ML classifiers have great utility in RV approaches and will lead to new subunit vaccines in the future.
Collapse
Affiliation(s)
- Ashley I Heinson
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK.
| | | | - Bastiaan Moesker
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK.
| | - Carmen C Denman Hume
- London School of Hygiene and Tropical Medicine (LSHTM), Department of Pathogen Molecular BiologyLondon WC1E 7HT, UK.
| | - Elena Vataga
- Solutions, University of Southampton, Southampton SO17 1BJ, UK.
| | - Yper Hall
- Public Health England, National Infection Service, Porton Down Salisbury, SP4 0JG, UK.
| | - Elena Stylianou
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK.
| | - Helen McShane
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK.
| | - Ann Williams
- Public Health England, National Infection Service, Porton Down Salisbury, SP4 0JG, UK.
| | - Mahesan Niranjan
- Department of Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, UK.
| | | |
Collapse
|
39
|
Choong YS, Lee YV, Soong JX, Law CT, Lim YY. Computer-Aided Antibody Design: An Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1053:221-243. [PMID: 29549642 DOI: 10.1007/978-3-319-72077-7_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of monoclonal antibody as the next generation protein therapeutics with remarkable success has surged the development of antibody engineering to design molecules for optimizing affinity, better efficacy, greater safety and therapeutic function. Therefore, computational methods have become increasingly important to generate hypotheses, interpret and guide experimental works. In this chapter, we discussed the overall antibody design by computational approches.
Collapse
Affiliation(s)
- Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia.
| | - Yie Vern Lee
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Jia Xin Soong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Cheh Tat Law
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| |
Collapse
|
40
|
Abstract
Antibodies are a group of proteins responsible for mediating immune reactions in vertebrates. They are able to bind a variety of structural motifs on noxious molecules tagging them for elimination from the organism. As a result of their versatile binding properties, antibodies are currently one of the most important classes of biopharmaceuticals. In this chapter, we discuss how knowledge-based computational methods can aid experimentalists in the development of potent antibodies. When using common experimental methods for antibody development, we often know the sequence of an antibody that binds to our molecule, antigen, of interest. We may also have a structure or model of the antigen. In these cases, computational methods can help by both modeling the antibody and identifying the antibody-antigen contact residues. This information can then play a key role in the rational design of more potent antibodies.
Collapse
Affiliation(s)
| | - James Dunbar
- Department of Statistics, University of Oxford, Oxford, UK
| | | |
Collapse
|
41
|
Potocnakova L, Bhide M, Pulzova LB. An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction. J Immunol Res 2016; 2016:6760830. [PMID: 28127568 PMCID: PMC5227168 DOI: 10.1155/2016/6760830] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/21/2016] [Accepted: 12/13/2016] [Indexed: 01/09/2023] Open
Abstract
Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes.
Collapse
Affiliation(s)
- Lenka Potocnakova
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
- Institute of Neuroimmunology of Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Lucia Borszekova Pulzova
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
| |
Collapse
|
42
|
Patwary NIA, Islam MS, Sohel M, Ara I, Sikder MOF, Shahik SM. In silico structure analysis and epitope prediction of E3 CR1-beta protein of Human Adenovirus E for vaccine design. Biomed J 2016; 39:382-390. [PMID: 28043417 PMCID: PMC6138513 DOI: 10.1016/j.bj.2016.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 07/12/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Human Adenoviruses are divided into 7 species of Human Adenovirus A to G based on DNA genome homology. The Human Adenovirus E (HAdVs-E) genome is a linear, double-stranded DNA containing 38 protein-coding genes. Wild-type adenoviruses type E, are linked to a number of slight illnesses. The most important part of HAdVs-E is E3 CR1-beta protein which controls the host immune response and viral attachment. METHOD We use numerous bio-informatics and immuno-informatics implements comprising sequence and construction tools for construction of 3D model and epitope prediction for HAdVs-E. RESULTS The 3D structure of E3 CR1-beta protein was generated and total of ten antigenic B cell epitopes, 6 MHC class I and 11 MHC class II binding peptides were predicted. CONCLUSION The study was carried out to predict antigenic determinants/epitopes of the E3 CR1-beta protein of Human Adenovirus E along with the 3D protein modeling. The study revealed potential T-cell and B-cell epitopes that can raise the desired immune response against E3 CR1-beta protein and useful in developing effective vaccines against HAdVs-E.
Collapse
Affiliation(s)
- Noman Ibna Amin Patwary
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Bangladesh
| | - Md Saiful Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Bangladesh
| | - Md Sohel
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Bangladesh
| | - Ismot Ara
- Department of Computer Science and Engineering, Faculty of Science and Technology, Atish Dipankar University of Science and Technology, Bangladesh; Department of Computer Science and Engineering, American International University-Bangladesh, Bangladesh
| | - Mohd Omar Faruk Sikder
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Bangladesh
| | - Shah Md Shahik
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Bangladesh.
| |
Collapse
|
43
|
Gaiotto T, Hufton SE. Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. PLoS One 2016; 11:e0164296. [PMID: 27741319 PMCID: PMC5065140 DOI: 10.1371/journal.pone.0164296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
Cross-neutralising monoclonal antibodies against influenza hemagglutinin (HA) are of considerable interest as both therapeutics and diagnostic tools. We have recently described five different single domain antibodies (nanobodies) which share this cross-neutralising activity and suggest their small size, high stability, and cleft binding properties may present distinct advantages over equivalent conventional antibodies. We have used yeast display in combination with deep mutational scanning to give residue level resolution of positions in the antibody-HA interface which are crucial for binding. In addition, we have mapped positions within HA predicted to have minimal effect on antibody binding when mutated. Our cross-neutralising nanobodies were shown to bind to a highly conserved pocket in the HA2 domain of A(H1N1)pdm09 influenza virus overlapping with the fusion peptide suggesting their mechanism of action is through the inhibition of viral membrane fusion. We also note that the epitope overlaps with that of CR6261 and F10 which are human monoclonal antibodies in clinical development as immunotherapeutics. Although all five nanobodies mapped to the same highly conserved binding pocket we observed differences in the size of the epitope footprint which has implications in comparing the relative genetic barrier each nanobody presents to a rapidly evolving influenza virus. To further refine our epitope map, we have re-created naturally occurring mutations within this HA stem epitope and tested their effect on binding using yeast display. We have shown that a D46N mutation in the HA2 stem domain uniquely interferes with binding of R2b-E8. Further testing of this substitution in the context of full length purified HA from 1918 H1N1 pandemic (Spanish flu), 2009 H1N1 pandemic (swine flu) and highly pathogenic avian influenza H5N1 demonstrated binding which correlated with D46 whereas binding to seasonal H1N1 strains carrying N46 was absent. In addition, our deep sequence analysis predicted that binding to the emerging H1N1 strain (A/Christchurch/16/2010) carrying the HA2-E47K mutation would not affect binding was confirmed experimentally. This demonstrates yeast display, in combination with deep sequencing, may be able to predict antibody reactivity to emerging influenza strains so assisting in the preparation for future influenza pandemics.
Collapse
Affiliation(s)
- Tiziano Gaiotto
- Biotherapeutics Group, National Institute for Biological Standards and Control, a centre of the Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar, Herts, EN6 3QG, United Kingdom
| | - Simon E. Hufton
- Biotherapeutics Group, National Institute for Biological Standards and Control, a centre of the Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar, Herts, EN6 3QG, United Kingdom
- * E-mail:
| |
Collapse
|
44
|
High Resolution Mapping of Bactericidal Monoclonal Antibody Binding Epitopes on Staphylococcus aureus Antigen MntC. PLoS Pathog 2016; 12:e1005908. [PMID: 27689696 PMCID: PMC5045189 DOI: 10.1371/journal.ppat.1005908] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
Abstract
The Staphylococcus aureus manganese transporter protein MntC is under investigation as a component of a prophylactic S.aureus vaccine. Passive immunization with monoclonal antibodies mAB 305-78-7 and mAB 305-101-8 produced using MntC was shown to significantly reduce S. aureus burden in an infant rat model of infection. Earlier interference mapping suggested that a total of 23 monoclonal antibodies generated against MntC could be subdivided into three interference groups, representing three independent immunogenic regions. In the current work binding epitopes for selected representatives of each of these interference groups (mAB 305-72-5 – group 1, mAB 305-78-7 – group 2, and mAB 305-101-8 – group 3) were mapped using Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS). All of the identified epitopes are discontinuous, with binding surface formed by structural elements that are separated within the primary sequence of the protein but adjacent in the context of the three-dimensional structure. The approach was validated by co-crystallizing the Fab fragment of one of the antibodies (mAB 305-78-7) with MntC and solving the three-dimensional structure of the complex. X-ray results themselves and localization of the mAB 305-78-7 epitope were further validated using antibody binding experiments with MntC variants containing substitutions of key amino acid residues. These results provided insight into the antigenic properties of MntC and how these properties may play a role in protecting the hostagainst S. aureus infection by preventing the capture and transport of Mn2+, a key element that the pathogen uses to evade host immunity. Staphylococcus aureus protein MntC is a metal-binding protein of the ABC-type transporter involved in the acquisition of an essential nutrient, Mn2+, by the pathogen. An earlier study demonstrated that use of MntC as an antigen in experimental vaccine can provide protection against staphylococcal infections in animals and identified three groups of protective monoclonal antibodies induced by the protein. In the current work we employed Deuterium-Hydrogen Exchange Mass Spectrometry (DXMS) to determine binding sites of selected representatives from each of those three groups. DXMS results were further validated using X-ray crystallography, site-directed mutagenesis and functional studies. Locations of the binding sites and results of the functional studies were used to draw conclusion on molecular mechanisms of protection afforded by MntC: antibodies belonging to two of the groups are predicted to interfere with Mn2+ transfer from the protein to the transmembrane channel pore, while the third group of the antibodies is expected to interfere with Mn2+ binding to MntC itself. The net result in both cases is impaired Mn2+ transport across the bacterial membrane and increased susceptibility of the bacterium to the oxidative stress, likely due to the reduced activity of superoxide dismutase which requires Mn2+ as an essential co-factor for activity.
Collapse
|
45
|
Wu CH, Liu IJ, Lu RM, Wu HC. Advancement and applications of peptide phage display technology in biomedical science. J Biomed Sci 2016; 23:8. [PMID: 26786672 PMCID: PMC4717660 DOI: 10.1186/s12929-016-0223-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 01/11/2016] [Indexed: 12/25/2022] Open
Abstract
Combinatorial phage library is a powerful research tool for high-throughput screening of protein interactions. Of all available molecular display techniques, phage display has proven to be the most popular approach. Screening phage-displayed random peptide libraries is an effective means of identifying peptides that can bind target molecules and regulate their function. Phage-displayed peptide libraries can be used for (i) B-cell and T-cell epitope mapping, (ii) selection of bioactive peptides bound to receptors or proteins, disease-specific antigen mimics, peptides bound to non-protein targets, cell-specific peptides, or organ-specific peptides, and (iii) development of peptide-mediated drug delivery systems and other applications. Targeting peptides identified using phage display technology may be useful for basic research and translational medicine. In this review article, we summarize the latest technological advancements in the application of phage-displayed peptide libraries to applied biomedical sciences.
Collapse
Affiliation(s)
- Chien-Hsun Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - I-Ju Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ruei-Min Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
| |
Collapse
|
46
|
Esmaielbeiki R, Krawczyk K, Knapp B, Nebel JC, Deane CM. Progress and challenges in predicting protein interfaces. Brief Bioinform 2016; 17:117-31. [PMID: 25971595 PMCID: PMC4719070 DOI: 10.1093/bib/bbv027] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/18/2015] [Indexed: 12/31/2022] Open
Abstract
The majority of biological processes are mediated via protein-protein interactions. Determination of residues participating in such interactions improves our understanding of molecular mechanisms and facilitates the development of therapeutics. Experimental approaches to identifying interacting residues, such as mutagenesis, are costly and time-consuming and thus, computational methods for this purpose could streamline conventional pipelines. Here we review the field of computational protein interface prediction. We make a distinction between methods which address proteins in general and those targeted at antibodies, owing to the radically different binding mechanism of antibodies. We organize the multitude of currently available methods hierarchically based on required input and prediction principles to provide an overview of the field.
Collapse
|
47
|
Kratsch C, Klingen TR, Mümken L, Steinbrück L, McHardy AC. Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses. Virus Evol 2016; 2:vev025. [PMID: 27774294 PMCID: PMC4989879 DOI: 10.1093/ve/vev025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human influenza viruses are rapidly evolving RNA viruses that cause short-term respiratory infections with substantial morbidity and mortality in annual epidemics. Uncovering the general principles of viral coevolution with human hosts is important for pathogen surveillance and vaccine design. Protein regions are an appropriate model for the interactions between two macromolecules, but the currently used epitope definition for the major antigen of influenza viruses, namely hemagglutinin, is very broad. Here, we combined genetic, evolutionary, antigenic, and structural information to determine the most relevant regions of the hemagglutinin of human influenza A/H3N2 viruses for interaction with human immunoglobulins. We estimated the antigenic weights of amino acid changes at individual sites from hemagglutination inhibition data using antigenic tree inference followed by spatial clustering of antigenicity-altering protein sites on the protein structure. This approach determined six relevant areas (patches) for antigenic variation that had a key role in the past antigenic evolution of the viruses. Previous transitions between successive predominating antigenic types of H3N2 viruses always included amino acid changes in either the first or second antigenic patch. Interestingly, there was only partial overlap between the antigenic patches and the patches under strong positive selection. Therefore, besides alterations of antigenicity, other interactions with the host may shape the evolution of human influenza A/H3N2 viruses.
Collapse
Affiliation(s)
- Christina Kratsch
- Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany and
| | - Thorsten R. Klingen
- Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany and
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Linda Mümken
- Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany and
| | - Lars Steinbrück
- Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany and
| | - Alice C. McHardy
- Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany and
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| |
Collapse
|
48
|
Dimitrov I, Atanasova M, Patronov A, Flower DR, Doytchinova I. A Cohesive and Integrated Platform for Immunogenicity Prediction. Methods Mol Biol 2016; 1404:761-770. [PMID: 27076336 DOI: 10.1007/978-1-4939-3389-1_50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In silico methods for immunogenicity prediction mine the enormous quantity of data arising from deciphered genomes and proteomes to identify immunogenic proteins. While high and productive immunogenicity is essential for vaccines, therapeutic proteins and monoclonal antibodies should be minimally immunogenic. Here, we present a cohesive platform for immunogenicity and MHC class I and/or II binding affinity prediction. The platform integrates three quasi-independent modular servers: VaxiJen, EpiJen, and EpiTOP. VaxiJen (http://www.ddg-pharmfac.net/vaxijen) predicts immunogenicity of proteins of different origin; EpiJen (http://www.ddg-pharmfac.net/epijen) predicts peptide binding to MHC class I proteins; and EpiTOP (http://www.ddg-pharmfac.net/epitop) predicts peptide binding to MHC class II proteins. The platform is freely accessible and user-friendly. The protocol for immunogenicity prediction is demonstrated by selecting immunogenic proteins from Mycobacterium tuberculosis and predicting how the peptide epitopes within them bind to MHC class I and class II proteins.
Collapse
Affiliation(s)
- Ivan Dimitrov
- School of Pharmacy, Medical University of Sofia, Sofia, 1000, Bulgaria
| | | | - Atanas Patronov
- Center for Integrated Protein Science Munich (CIPSM), Technical University of Munich, Freising-Weihenstephan, 85354, Germany.,Department of Life Sciences, Technical University of Munich, Freising-Weihenstephan, 85354, Germany
| | - Darren R Flower
- School of Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK
| | - Irini Doytchinova
- School of Pharmacy, Medical University of Sofia, Sofia, 1000, Bulgaria.
| |
Collapse
|
49
|
Zhang C, Li Y, Tang W, Zhou Z, Sun P, Ma Z. The Relationship between B-cell Epitope and Mimotope Sequences. Protein Pept Lett 2016; 23:132-41. [PMID: 26715528 PMCID: PMC5427807 DOI: 10.2174/0929866523666151230124538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/30/2015] [Accepted: 11/23/2015] [Indexed: 11/22/2022]
Abstract
B-cell epitope is a group of residues which is on the surface of an antigen. It invokes humoral responses. Locating B-cell epitope is important for effective vaccine design, and the development of diagnostic reagents. Mimotope-based B-cell epitope prediction method is a kind of conformational B-cell epitope prediction, and the core idea of the method is mapping the mimotope sequences which are obtained from a random phage display library. However, current mimotope-based B-cell epitope prediction methods cannot maintain a high degree of satisfaction in the circumstances of employing only mimotope sequences. In this study, we did a multi-perspective analysis on parameters for conformational B-cell epitopes and characteristics between epitope and mimotope on a benchmark datasets which contains 67 mimotope sets, corresponding to 40 unique complex structures. In these 67 cases, there are 25 antigen-antibody complexes and 42 protein-protein interactions. We analyzed the two parts separately. The results showed the mimotope sequences do have some epitope features, but there are also some epitope properties that mimotope sequences do not contain. In addition, the numbers of epitope segments with different lengths were obviously different between the antigen-antibody complexes and the protein-protein interactions. This study reflects how similar do mimotope sequence and genuine epitopes have; and evaluates existing mimotope-based B-cell epitope prediction methods from a novel viewpoint.
Collapse
Affiliation(s)
- Chunhua Zhang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Yunyun Li
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Ganjingzi District Dalian City Hengyuan Primary School, Dalian 116000, China
| | - Weina Tang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Zhiguo Zhou
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
| | - Pingping Sun
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Zhiqiang Ma
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| |
Collapse
|
50
|
Interferon Beta: From Molecular Level to Therapeutic Effects. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 326:343-72. [DOI: 10.1016/bs.ircmb.2016.06.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|