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Aghamolaei S, Mamaghani AJ, Ashrafi K, Kazemi B, Bandehpour M, Rouhani S, Rashidi S, Tabaei SJS. Designing and Developing Serological Test for the Diagnosis of Human Fascioliasis Using a New Recombinant Multi-epitope. Acta Parasitol 2024; 69:1005-1015. [PMID: 38498251 DOI: 10.1007/s11686-024-00796-0] [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: 05/24/2023] [Accepted: 01/12/2024] [Indexed: 03/20/2024]
Abstract
PURPOSE Fascioliasis is a common parasitic disease in humans and herbivores which is caused by Fasciola hepatica and Fasciola gigantica and has a worldwide distribution. Serological tests such as the enzyme-linked immunosorbent assay (ELISA) technique play a prominent role in the fast diagnosis of the disease. However, there are diagnostic limitations, including cross-reactivity with other worms, which decline the specificity of the results. This study aimed to evaluate the structure of a recombinant multi-epitope antigen produced from linear and conformational B-cell epitopes of three parasitic proteins with sera of individuals with fasciolosis, healthy controls, and those with other diseases to gain accurate sensitivity and specificity. METHODS After designing the multi-epitope structure of cathepsin L1, FhTP16.5, and SAP-2 antigens and then synthesizing, cloning, and expressing, the extracted purified protein was evaluated by indirect ELISA to detect IgG antibodies against Fasciola hepatica parasite among the sera of 39 serum samples of Fasciola hepatica, 35 healthy individual samples, and 20 samples of other types of parasitic diseases. The synthesized multi-epitope produced from cathepsin L1, FhTP16.5, and SAP-2 antigens was evaluated using the indirect ELISA. RESULTS The analysis of the samples mentioned for IgG antibody diagnosis against Fasciola hepatica showed 97.43% (95% confidence interval, 94.23-100%) sensitivity and 100% (95% confidence interval, 97-100%) specificity. CONCLUSION The recombinant B-cell multi-epitope with high antigenic potency may increase the specificity of epitopic peptides and ultimately help improve and develop indirect ELISA commercial kits for the diagnosis of fascioliasis in humans.
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Affiliation(s)
- Somayeh Aghamolaei
- Department of Parasitology and Mycology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Amirreza Javadi Mamaghani
- Hepatitis Research Center, Department of Medical Parasitology and Mycology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Keyhan Ashrafi
- Department of Medical Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, ShahidBeheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, ShahidBeheshti University of Medical Sciences, Tehran, Iran
| | - Soheila Rouhani
- Department of Parasitology and Mycology, ShahidBeheshti University of Medical Sciences, Tehran, Iran
| | - Sama Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Ali A, Ahmad S, de Albuquerque PMM, Kamil A, Alshammari FA, Alouffi A, da Silva Vaz I. Prediction of Novel Drug Targets and Vaccine Candidates against Human Lice (Insecta), Acari (Arachnida), and Their Associated Pathogens. Vaccines (Basel) 2021; 10:vaccines10010008. [PMID: 35062669 PMCID: PMC8778234 DOI: 10.3390/vaccines10010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/12/2023] Open
Abstract
The emergence of drug-resistant lice, acari, and their associated pathogens (APs) is associated with economic losses; thus, it is essential to find new appropriate therapeutic approaches. In the present study, a subtractive proteomics approach was used to predict suitable therapeutics against these vectors and their infectious agents. We found 9701 proteins in the lice (Pediculus humanus var. corporis) and acari (Ixodes scapularis, Leptotrombidium deliense), and 4822 proteins in the proteomes of their APs (Babesia microti, Borreliella mayonii, Borrelia miyamotoi, Borrelia recurrentis, Rickettsia prowazekii, Orientia tsutsugamushi str. Boryong) that were non-homologous to host proteins. Among these non-homologous proteins, 365 proteins of lice and acari, and 630 proteins of APs, were predicted as essential proteins. Twelve unique essential proteins were predicted to be involved in four unique metabolic pathways of lice and acari, and 103 unique proteins were found to be involved in 75 unique metabolic pathways of APs. The sub cellular localization analysis of 115 unique essential proteins of lice and acari and their APs revealed that 61 proteins were cytoplasmic, 42 as membrane-bound proteins and 12 proteins with multiple localization. The druggability analysis of the identified 73 cytoplasmic and multiple localization essential proteins revealed 22 druggable targets and 51 novel drug targets that participate in unique pathways of lice and acari and their APs. Further, the predicted 42 membrane bound proteins could be potential vaccine candidates. Screening of useful inhibitors against these novel targets may result in finding novel compounds efficient for the control of these parasites.
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Affiliation(s)
- Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
| | - Shabir Ahmad
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
| | | | - Atif Kamil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
| | - Fahdah Ayed Alshammari
- College of Sciences and Literature Microbiology, Nothern Border University, Rafha 76413, Saudi Arabia;
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia;
- Vaccines Research for Infectious Diseases, King Saud University, Riyadh 11495, Saudi Arabia
- Veterinary Laboratories and Vaccines Center, Ministry of Environment Water & Agriculture, Riyadh 11195, Saudi Arabia
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
- Correspondence: ; Tel.: +55-(51)-33086078; Fax: +55-(51)-33087309
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Jamal F, Singh MK, Hansa J, Pushpanjali, Ahmad G, Dikhit MR, Umar MS, Bimal S, Das P, Mujeeb AA, Singh SK, Zubair S, Owais M. Leishmania-Specific Promiscuous Membrane Protein Tubulin Folding Cofactor D Divulges Th 1/Th 2 Polarization in the Host via ERK -1/2 and p38 MAPK Signaling Cascade. Front Immunol 2020; 11:817. [PMID: 32582140 PMCID: PMC7280453 DOI: 10.3389/fimmu.2020.00817] [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: 10/23/2019] [Accepted: 04/09/2020] [Indexed: 11/24/2022] Open
Abstract
Visceral leishmaniasis (VL)-related mortality and morbidity imposes a great deal of health concern across the globe. The existing anti-leishmanial drug regimen generally fails to eliminate newly emerging resistant isolates of this dreadful parasite. In such circumstances, the development of a prophylactic strategy to impart protection against the disease is likely to take center stage. In order to develop a promising prophylactic vaccine, it is desirable to identify an adequately potential vaccine candidate. In silico analysis of Leishmania tubulin folding cofactor D protein predicted its potential to activate both B- and T-cell repertoires. Furthermore, the ELISA employing anti-peptide27 (a segment of tubulin folding cofactor D) antibody revealed its proficiency in VL diagnosis and treatment monitoring. The peptide27 and its cocktail with another Leishmania peptide (peptide23) prompted the up-regulation of pro-inflammatory cytokines, such as IFN-γ, TNF-α, IL-2, IL-17, etc., and the down-regulation of immune-regulatory cytokines, such as IL-10, in the immunized BALB/c mice. Coherent to the consequence of peptide-specific humoral immune response, peptide cocktail-based immunization ensued in the predominant amplification of pathogen-specific IgG2a over the IgG1 isotype, up-regulated proliferation of T lymphocytes, and enhanced production of nitric oxide, reactive oxygen species, etc. We also established that the peptide cocktail modulated host MAPK signaling to favor the amplification of Th1-dominated immune response in the host. The peptide cocktail mediated the activation of the host immune armory, which was eventually translated into a significant decline in parasitic load in the visceral organs of experimental animals challenged with Leishmania donovani.
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Affiliation(s)
- Fauzia Jamal
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Manish K Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Jagadish Hansa
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pushpanjali
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Ghufran Ahmad
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Mohd Saad Umar
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Sanjiva Bimal
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Anzar Abdul Mujeeb
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Shubhankar K Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Swaleha Zubair
- Department of Computer Science, Aligarh Muslim University, Aligarh, India
| | - Mohammad Owais
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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Ndawula C, Amaral Xavier M, Villavicencio B, Cortez Lopes F, Juliano MA, Parizi LF, Verli H, da Silva Vaz I, Ligabue-Braun R. Prediction, mapping and validation of tick glutathione S-transferase B-cell epitopes. Ticks Tick Borne Dis 2020; 11:101445. [PMID: 32354639 DOI: 10.1016/j.ttbdis.2020.101445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 04/02/2020] [Accepted: 04/10/2020] [Indexed: 10/24/2022]
Abstract
In search of ways to address the increasing incidence of global acaricide resistance, tick control through vaccination is regarded as a sustainable alternative approach. Recently, a novel cocktail antigen tick-vaccine was developed based on the recombinant glutathione S-transferase (rGST) anti-sera cross-reaction to glutathione S-transferases of Rhipicephalus appendiculatus (GST-Ra), Amblyomma variegatum (GST-Av), Haemaphysalis longicornis (GST-Hl), Rhipicephalus decoloratus (GST-Rd) and Rhipicephalus microplus (GST-Rm). Therefore, the current study aimed to predict the shared B-cell epitopes within the GST sequences of these tick species. Prediction of B-cell epitopes and proteasomal cleavage sites were performed using immunoinformatics algorithms. The conserved epitopes predicted within the sequences were mapped on the homodimers of the respective tick GSTs, and the corresponding peptides were independently used for rabbit immunization experiments. Based on the dot blot assay, the immunogenicity of the peptides and their potential to be recognized by corresponding rGST anti-sera raised by rabbit immunization in a previous work were investigated. This study revealed that the predicted conserved B-cell epitopes within the five tick GST sequences were localized on the surface of the respective GST homodimers. The epitopes of GST-Ra, GST-Rd, GST-Av, and GST-Hl were also shown to contain a seven residue-long peptide sequence with no proteasomal cleavage sites, whereas proteasomal digestion of GST-Rm was predicted to yield a 4-residue fragment. Given that a few proteasomal cleavage sites were found within the conserved epitope sequences of the four GSTs, the sequences could also contain a T-cell epitope. Finally, the peptide and rGST anti-sera reacted against the corresponding peptide, confirming their immunogenicity. These data support the claim that the rGSTs, used in the previous study, contain conserved B-cell epitopes, which elucidates why the rGST anti-sera cross-reacted to non-homologous tick GSTs. Taken together, the data suggest that the B-cell epitopes predicted in this study could be useful for constituting epitope-based GST tick vaccines.
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Affiliation(s)
- Charles Ndawula
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marina Amaral Xavier
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Bianca Villavicencio
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fernanda Cortez Lopes
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Aparecida Juliano
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Luís Fernando Parizi
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Departamento de Farmacociências, Universidade Federal das Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
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Design and expression of polytopic construct of cathepsin-L1, SAP-2 and FhTP16.5 proteins of Fasciola hepatica. J Helminthol 2020; 94:e134. [PMID: 32127056 DOI: 10.1017/s0022149x20000140] [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] [Indexed: 02/07/2023]
Abstract
The enzyme-linked immunosorbent assay (ELISA) technique can play an important role in the early detection of fascioliasis. However, they have some diagnostic limitations, including cross-reaction with other helminths. It seems that the combination of recombinant parasite proteins as antigen can reduce these problems. Hence, the present study was aimed to design and confirm the antigenic recombinant multi-epitope (rMEP) construct of three protein epitopes (linear and conformational B-cell epitopes) of the parasite using immunoinformatic tools. For this purpose, the tertiary structures of Fasciola hepatica cathepsin-L1, saposin-like protein 2 and 16.5-kDa tegument-associated protein were predicted using the I-TASSER server. Validation of the modelled structures was performed by Ramachandran plots. The antigenic epitopes of the proteins were achieved by analysing the features of the IEDB server. The synthesized gene was cloned into the pET-22b (+) expression vector and transformed into the Escherichia coli BL21. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was used to verify and analyse the expression of the rMEP protein. Western blotting was utilized to confirm rMEP protein immunogenicity in two forms, one using an anti-His tag antibody and the other with human pooled sera samples (fascioliasis, non-fascioliasis and negative control sera). Our results demonstrated that the rMEP designed for the three proteins of F. hepatica was highly antigenic, and immune-detection techniques confirmed the antigen specificity. In conclusion, the presented antigenic multi-epitope may be very helpful to develop serodiagnostic kits such as indirect ELISA to evaluate the proper diagnosis of fascioliasis in humans and ruminants.
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Saadat S, Alikhani MY, Rikhtegaran Tehrani Z, Yousefi Mashouf R. Computational design of a new chimeric protein for sero-diagnosis of Mycoplasma hominis. GAZZETTA MEDICA ITALIANA ARCHIVIO PER LE SCIENZE MEDICHE 2019. [DOI: 10.23736/s0393-3660.18.03900-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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In silico homology modelling and prediction of novel epitopic peptides from P24 protein of Haemonchus contortus. Gene 2019; 703:102-111. [DOI: 10.1016/j.gene.2019.03.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/23/2019] [Accepted: 03/25/2019] [Indexed: 01/02/2023]
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Tarahomjoo S, Ghaderi S. In silico Design of a Novel Serotype Independent Vaccine Against Streptococcus pneumoniae Based on B-cell Epitope Regions of Fibronectin Binding Protein, Choline Binding Protein D, and D-alanyl-D-alanine Carboxypeptidase. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180815150600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Pneumococcal conjugate vaccines (PCVs) in the past, have been constructed via chemical coupling of pneumococcal capsules to immunogenic carrier proteins. The PCVs implementation in developing countries was prevented by their high manufacturing costs. This issue can be overcome via the development of protein-based vaccines against pneumococci. Choline binding protein D (CBPD), fibronectin binding protein (FBP), and D-alanyl-D-alanine-carboxy peptidase (DDCP) were already identified as pneumococcal surface proteins able to elicit protection against S. pneumoniae serotype 19F.Methods:As antibody responses are necessary for protection against pneumococci, the aim of this study is, therefore, to design computationally a chimeric pneumococcal vaccine using B-cell epitope regions of CBPD, FBP, and DDCP. These regions were determined using results of Bepipred, BCPreds and CBTope programs. The most probable immunoprotective B-cell epitope region (MIBR) of each protein was identified using VaxiJen. MIBRs were highly conserved in common S. pneumoniae serotypes causing invasive pneumococcal disease worldwide. The conserved MIBRs were joined together using either flexible (Gly4Ser)2 linker or the rigid AspProArgValProSerSer linker to form antigens with molecular weights of 22.53 kDa and 22.74 kDa, respectively.Results and Discussion:The codon optimization was done for the chimeric antigens. Analysis of mRNAs secondary structures revealed no stable hairpins at 5' ends that could interfere with antigen expression. The 3D model of the antigen possessing the flexible linker contained alpha helix, whereas several beta sheets were observed in the tertiary structure of the antigen possessing the rigid linker and it did not have any alpha helixes. Moreover, the antigen-containing the rigid linker included a beta sheet in the C-terminus of DDCP MIBR, which showed 60% residue identity to the beta sheet in the same region of the partial structure of DDCP obtained from protein data bank. However, the other antigen did not contain any similar structural elements in DDCP MIBR.Conclusion:In silico analyses of physicochemical properties indicated that inclusion of the rigid linker instead of the flexible linker resulted in better stability of the chimeric antigen. In addition, using the rigid linker increased the probability of the protein soluble expression in Escherichia coli. Therefore, the chimeric antigen composed of conserved MIBRs joining via the rigid linker is predicted to be a suitable vaccine candidate, which could elicit protection against common pneumococcal serotypes.
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Affiliation(s)
- Shirin Tarahomjoo
- Division of Genomics and Genetic Engineering, Department of Biotechnology and Central Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran
| | - Soheila Ghaderi
- Division of Central Laboratory, Department of Biotechnology and Central Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran
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Nagpal G, Chaudhary K, Agrawal P, Raghava GPS. Computer-aided prediction of antigen presenting cell modulators for designing peptide-based vaccine adjuvants. J Transl Med 2018; 16:181. [PMID: 29970096 PMCID: PMC6029051 DOI: 10.1186/s12967-018-1560-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/23/2018] [Indexed: 11/26/2022] Open
Abstract
Background Evidences in literature strongly advocate the potential of immunomodulatory peptides for use as vaccine adjuvants. All the mechanisms of vaccine adjuvants ensuing immunostimulatory effects directly or indirectly stimulate antigen presenting cells (APCs). While numerous methods have been developed in the past for predicting B cell and T-cell epitopes; no method is available for predicting the peptides that can modulate the APCs. Methods We named the peptides that can activate APCs as A-cell epitopes and developed methods for their prediction in this study. A dataset of experimentally validated A-cell epitopes was collected and compiled from various resources. To predict A-cell epitopes, we developed support vector machine-based machine learning models using different sequence-based features. Results A hybrid model developed on a combination of sequence-based features (dipeptide composition and motif occurrence), achieved the highest accuracy of 95.71% with Matthews correlation coefficient (MCC) value of 0.91 on the training dataset. We also evaluated the hybrid models on an independent dataset and achieved a comparable accuracy of 95.00% with MCC 0.90. Conclusion The models developed in this study were implemented in a web-based platform VaxinPAD to predict and design immunomodulatory peptides or A-cell epitopes. This web server available at http://webs.iiitd.edu.in/raghava/vaxinpad/ will facilitate researchers in designing peptide-based vaccine adjuvants. Electronic supplementary material The online version of this article (10.1186/s12967-018-1560-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gandharva Nagpal
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Kumardeep Chaudhary
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Piyush Agrawal
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Gajendra P S Raghava
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India. .,Centre for Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, 110020, India.
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Vakili B, Nezafat N, Hatam GR, Zare B, Erfani N, Ghasemi Y. Proteome-scale identification of Leishmania infantum for novel vaccine candidates: A hierarchical subtractive approach. Comput Biol Chem 2017; 72:16-25. [PMID: 29291591 DOI: 10.1016/j.compbiolchem.2017.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/16/2017] [Accepted: 12/18/2017] [Indexed: 01/06/2023]
Abstract
Vaccines are one of the most significant achievements in medical science. However, vaccine design is still challenging at all stages. The selection of antigenic peptides as vaccine candidates is the first and most important step for vaccine design. Experimental selection of antigenic peptides for the design of vaccines is a time-consuming, labor-intensive and expensive procedure. More recently, in the light of computer-aided biotechnology and reverse vaccinology, the precise selection of antigenic peptides and rational vaccine design against many pathogens have developed. In this study, the whole proteome of Leishmania infantum was analyzed using a pipeline of algorithms. From the set of 8045 proteins of L. infantum, sixteen novel antigenic proteins were derived using a hierarchical proteome subtractive analysis. These novel vaccine targets can be utilized as top candidates for designing the new prophylactic or therapeutic vaccines against visceral leishmaniasis. Significantly, all the sixteen novel vaccine candidates are non-allergen antigenic proteins that have not been used for the design of vaccines against visceral leishmaniasis until now.
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Affiliation(s)
- Bahareh Vakili
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholam Reza Hatam
- Basic Sciences in Infectious Diseases Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bijan Zare
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasrollah Erfani
- Institute for Cancer Research (ICR), School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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Peripheral T-Cell Reactivity to Heat Shock Protein 70 and Its Cofactor GrpE from Tropheryma whipplei Is Reduced in Patients with Classical Whipple's Disease. Infect Immun 2017; 85:IAI.00363-17. [PMID: 28559404 DOI: 10.1128/iai.00363-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 05/21/2017] [Indexed: 12/17/2022] Open
Abstract
Classical Whipple's disease (CWD) is characterized by the lack of specific Th1 response toward Tropheryma whipplei in genetically predisposed individuals. The cofactor GrpE of heat shock protein 70 (Hsp70) from T. whipplei was previously identified as a B-cell antigen. We tested the capacity of Hsp70 and GrpE to elicit specific proinflammatory T-cell responses. Peripheral mononuclear cells from CWD patients and healthy donors were stimulated with T. whipplei lysate or recombinant GrpE or Hsp70 before levels of CD40L, CD69, perforin, granzyme B, CD107a, and gamma interferon (IFN-γ) were determined in T cells by flow cytometry. Upon stimulation with total bacterial lysate or recombinant GrpE or Hsp70 of T. whipplei, the proportions of activated effector CD4+ T cells, determined as CD40L+ IFN-γ+, were significantly lower in patients with CWD than in healthy controls; CD8+ T cells of untreated CWD patients revealed an enhanced activation toward unspecific stimulation and T. whipplei-specific degranulation, although CD69+ IFN-γ+ CD8+ T cells were reduced upon stimulation with T. whipplei lysate and recombinant T. whipplei-derived proteins. Hsp70 and its cofactor GrpE are immunogenic in healthy individuals, eliciting effective responses against T. whipplei to control bacterial spreading. The lack of specific T-cell responses against these T. whipplei-derived proteins may contribute to the pathogenesis of CWD.
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In silico analysis and in vitro evaluation of immunogenic and immunomodulatory properties of promiscuous peptides derived from Leishmania infantum eukaryotic initiation factor. Bioorg Med Chem 2017; 25:5904-5916. [PMID: 28974324 DOI: 10.1016/j.bmc.2017.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 06/16/2017] [Accepted: 07/06/2017] [Indexed: 12/16/2022]
Abstract
It is generally considered as imperative the ability to control leishmaniasis through the development of a protective vaccine capable of inducing long-lasting and protective cell-mediated immune responses. In this current study, we demonstrated potential epitopes that bind to H2 MHC class I and II molecules by conducting the in silico analysis of Leishmania infantum eukaryotic Initiation Factor (LieIF) protein, using online available algorithms. Moreover, we synthesized five peptides (16-18 amino acids long) which are part of the N-terminal portion of LieIF and contain promising MHC class I and II-restricted epitopes and afterwards, their predicted immunogenicity was evaluated in vitro by monitoring peptide-specific T-cell responses. Additionally, the immunomodulatory properties of these peptides were investigated in vitro by exploring their potential of inducing phenotypic maturation and functional differentiation of murine Bone-Marrow derived Dendritic Cells (BM-DCs). It was revealed by our data that all the synthetic peptides predicted for H2 alleles; present the property of immunogenicity. Among the synthetic peptides which contained T-cell epitopes, the peptide 52-68 aa (LieIF_2) exhibited immunomodulatory properties with the larger potential. LieIF_2-pulsed BM-DCs up-regulated the expression of the co-stimulatory surface molecules CD80 and CD86, as well as the production of the proinflammatory cytokine TNF-α and of the Th1-polarizing cytokines IL-12 and IFN-γ. The aforementioned data suggest that selected parts of LieIF could be used to develop innovative subunit protective vaccines able to induce effective immunity mediated by MHC class I-restricted as well as class II-restricted T-cell responses.
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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: 197] [Impact Index Per Article: 24.6] [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.
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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
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Synthetic Peptides are Better Than Native Antigens for Development of ELISA Assay for Diagnosis of Tuberculosis. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-016-9556-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Han JH, Li J, Wang B, Lee SK, Nyunt MH, Na S, Park JH, Han ET. Identification of Immunodominant B-cell Epitope Regions of Reticulocyte Binding Proteins in Plasmodium vivax by Protein Microarray Based Immunoscreening. THE KOREAN JOURNAL OF PARASITOLOGY 2015; 53:403-11. [PMID: 26323838 PMCID: PMC4566507 DOI: 10.3347/kjp.2015.53.4.403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 07/23/2015] [Accepted: 07/23/2015] [Indexed: 11/23/2022]
Abstract
Plasmodium falciparum can invade all stages of red blood cells, while Plasmodium vivax can invade only reticulocytes. Although many P. vivax proteins have been discovered, their functions are largely unknown. Among them, P. vivax reticulocyte binding proteins (PvRBP1 and PvRBP2) recognize and bind to reticulocytes. Both proteins possess a C-terminal hydrophobic transmembrane domain, which drives adhesion to reticulocytes. PvRBP1 and PvRBP2 are large (> 326 kDa), which hinders identification of the functional domains. In this study, the complete genome information of the P. vivax RBP family was thoroughly analyzed using a prediction server with bioinformatics data to predict B-cell epitope domains. Eleven pvrbp family genes that included 2 pseudogenes and 9 full or partial length genes were selected and used to express recombinant proteins in a wheat germ cell-free system. The expressed proteins were used to evaluate the humoral immune response with vivax malaria patients and healthy individual serum samples by protein microarray. The recombinant fragments of 9 PvRBP proteins were successfully expressed; the soluble proteins ranged in molecular weight from 16 to 34 kDa. Evaluation of the humoral immune response to each recombinant PvRBP protein indicated a high antigenicity, with 38-88% sensitivity and 100% specificity. Of them, N-terminal parts of PvRBP2c (PVX_090325-1) and PvRBP2 like partial A (PVX_090330-1) elicited high antigenicity. In addition, the PvRBP2-like homologue B (PVX_116930) fragment was newly identified as high antigenicity and may be exploited as a potential antigenic candidate among the PvRBP family. The functional activity of the PvRBP family on merozoite invasion remains unknown.
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Affiliation(s)
- Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Jian Li
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.,Department of Parasitology, College of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Bo Wang
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.,Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Myat Htut Nyunt
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.,Department of Medical Research, Yangon, Myanmar
| | - Sunghun Na
- Department of Obstetrics and Gynecology, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Jeong-Hyun Park
- Department of Anatomy, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
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Nagpal G, Gupta S, Chaudhary K, Dhanda SK, Prakash S, Raghava GPS. VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants. Sci Rep 2015. [PMID: 26212482 PMCID: PMC4515643 DOI: 10.1038/srep12478] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Immunomodulatory oligodeoxynucleotides (IMODNs) are the short DNA sequences that activate the innate immune system via toll-like receptor 9. These sequences predominantly contain unmethylated CpG motifs. In this work, we describe VaccineDA (Vaccine DNA adjuvants), a web-based resource developed to design IMODN-based vaccine adjuvants. We collected and analyzed 2193 experimentally validated IMODNs obtained from the literature. Certain types of nucleotides (e.g., T, GT, TC, TT, CGT, TCG, TTT) are dominant in IMODNs. Based on these observations, we developed support vector machine-based models to predict IMODNs using various compositions. The developed models achieved the maximum Matthews Correlation Coefficient (MCC) of 0.75 with an accuracy of 87.57% using the pentanucleotide composition. The integration of motif information further improved the performance of our model from the MCC of 0.75 to 0.77. Similarly, models were developed to predict palindromic IMODNs and attained a maximum MCC of 0.84 with the accuracy of 91.94%. These models were evaluated using a five-fold cross-validation technique as well as validated on an independent dataset. The models developed in this study were integrated into VaccineDA to provide a wide range of services that facilitate the design of DNA-based vaccine adjuvants (http://crdd.osdd.net/raghava/vaccineda/).
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Affiliation(s)
- Gandharva Nagpal
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, INDIA
| | - Sudheer Gupta
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, INDIA
| | - Kumardeep Chaudhary
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, INDIA
| | - Sandeep Kumar Dhanda
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, INDIA
| | - Satya Prakash
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, INDIA
| | - Gajendra P S Raghava
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, INDIA
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