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Halabian R, Jahangiri A, Sedighian H, Behzadi E, Fooladi AAI. Staphylococcal enterotoxin B as DNA vaccine against breast cancer in a murine model. Int Microbiol 2023; 26:939-949. [PMID: 36991248 PMCID: PMC10057679 DOI: 10.1007/s10123-023-00348-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023]
Abstract
Recently, many efforts have been made to treat cancer using recombinant bacterial toxins and this strategy has been used in clinical trials of various cancers. Therapeutic DNA cancer vaccines are now considered as a promising strategy to activate the immune system against cancer. Cancer vaccines could induce specific and long-lasting immune responses against tumors. This study aimed to evaluate the antitumor potency of the SEB DNA vaccine as a new antitumor candidate against breast tumors in vivo. To determine the effect of the SEB construct on inhibiting tumor cell growth in vivo, the synthetic SEB gene, subsequent codon optimization, and embedding the cleavage sites were sub-cloned to an expression vector. Then, SEB construct, SEB, and PBS were injected into the mice. After being vaccinated, 4T1 cancer cells were injected subcutaneously into the right flank of mice. Then, the cytokine levels of IL-4 and IFN-γ were estimated by the ELISA method to evaluate the antitumor activity. The spleen lymphocyte proliferation, tumor size, and survival time were assessed. The concentration of IFN-γ in the SEB-Vac group showed a significant increase compared to other groups. The production of IL-4 in the group that received the DNA vaccine did not change significantly compared to the control group. The lymphocyte proliferation increased significantly in the mice group that received SEB construct than PBS control group (p < 0.001). While there was a meaningful decrease in tumor size (p < 0.001), a significant increase in tumor tissue necrosis (p < 0.01) and also in survival time of the animal model receiving the recombinant construct was observed. The designed SEB gene construct can be a new model vaccine for breast cancer because it effectively induces necrosis and produces specific immune responses. This structure does not hurt normal cells and is a safer treatment than chemotherapy and radiation therapy. Its slow and long-term release gently stimulates the immune system and cellular memory. It could be applied as a new model for inducing apoptosis and antitumor immunity to treat cancer.
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Affiliation(s)
- Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hamid Sedighian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Elham Behzadi
- Academy of Medical Sciences of the I.R. of Iran, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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In Silico Prediction of T and B Cell Epitopes of SAG1-Related Sequence 3 (SRS3) Gene for Developing Toxoplasma gondii Vaccine. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.69241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
: Toxoplasmosis is a worldwide infection that can lead to serious problems in immune-compromised individuals and fetuses. A DNA vaccine strategy would be an ideal tool against Toxoplasma gondii. One of the necessary measures to provide an effective vaccine is the selection of proteins with high antigenicity. The SAG1-related sequence 3 (SRS3) protein is a major surface antigen in T. gondii that can be used as a vaccine candidate. In the present study, bioinformatics and computational methods were utilized to predict protein characteristics, as well as secondary and tertiary structures. The in silico approach is highly suited to analyze, design, and evaluate DNA vaccine strategies. Hence, in silico prediction was used to identify B and T cell epitopes and compare the antigenicity of SRS3 and other candidate genes of Toxoplasma previously applied in the production of vaccines. The results of the analysis theoretically showed that SRS3 has multiple epitopes with high antigenicity, proposing that SRS3 is a promising immunogenic candidate for the development of DNA vaccines against toxoplasmosis.
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Sefidi-Heris Y, Jahangiri A, Mokhtarzadeh A, Shahbazi MA, Khalili S, Baradaran B, Mosafer J, Baghbanzadeh A, Hejazi M, Hashemzaei M, Hamblin MR, Santos HA. Recent progress in the design of DNA vaccines against tuberculosis. Drug Discov Today 2020; 25:S1359-6446(20)30345-7. [PMID: 32927065 DOI: 10.1016/j.drudis.2020.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/31/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022]
Abstract
Current tuberculosis (TB) vaccines have some disadvantages and many efforts have been undertaken to produce effective TB vaccines. As a result of their advantages, DNA vaccines are promising future vaccine candidates. This review focuses on the design and delivery of novel DNA-based vaccines against TB.
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Affiliation(s)
- Youssof Sefidi-Heris
- Department of Biology, College of Sciences, Shiraz University, 7146713565, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, 193955487, Tehran, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran.
| | - Mohammad-Ali Shahbazi
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland; Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC), Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran.
| | - Saeed Khalili
- Department of Biology Sciences, Faculty of Sciences, Shahid Rajaee Teacher Training University, 1678815811, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran
| | - Jafar Mosafer
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, 9516915169, Torbat Heydariyeh, Iran; Nanotechnology Research Center, School of Pharmacy, Mashhad University of Medical Sciences, 9196773117, Mashhad, Iran
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran
| | - Maryam Hejazi
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran
| | - Mahmoud Hashemzaei
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Zabol University of Medical Sciences, 9861615881, Zabol, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa.
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland; Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki FI-00014, Finland.
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In Silico Design of Multi-Epitope ESAT-6:Ag85b:Fcγ2a Fusion Protein as a Novel Candidate for Tuberculosis Vaccine. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.90449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
: Mycobacterium tuberculosis (MTB), which is the causative agent of tuberculosis (TB), is among the most important infectious bacteria with high morbidity and mortality rates worldwide. Bacilli Calmette-Guerin (BCG) vaccine has been discovered for about a century, and it is considered as a major vaccine for humans. However, some factors, such as its attenuated nature and its inefficacy against the latent form of the disease, have led to the use of alternative vaccines. Multi-epitope subunit vaccines are new-generation vaccines that are being developed in clinical trial phases. For the production of a subunit vaccine, the selection of immunodominant antigens and targeted delivery systems to antigen presenting cells (APCs) are considered as basic parameters. In the present study, we designed the novel multi-epitope ESAT-6:Ag85B:Fcγ2a, which was evaluated completely by various online tools as an optimum vaccine against TB. The early secreted antigenic target of 6 kDa (ESAT-6) and antigen 85B (Ag85B) are two immunodominant antigens, and Fcγ2a is a targeted delivery system. This vaccine candidate can be used for future preclinical studies.
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Sefid F, Baghban R, Payandeh Z, Khalesi B, Mahmoudi Gomari M. Structure Evaluation of IroN for Designing a Vaccine against Escherichia Coli, an In Silico Approach. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2019. [DOI: 10.29252/jommid.7.4.93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Slathia PS, Sharma P. A common conserved peptide harboring predicted T and B cell epitopes in domain III of envelope protein of Japanese Encephalitis Virus and West Nile Virus for potential use in epitope based vaccines. Comp Immunol Microbiol Infect Dis 2019; 65:238-245. [PMID: 31300121 DOI: 10.1016/j.cimid.2019.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
Japanese encephalitis virus (JEV) and West Nile virus (WNV) are two major mosquito borne flaviviruses belonging to same serocomplex. JEV is transmitted by Culex mosquitoes and the reservoir host for the virus is pigs and/or water birds. WNV is also transmitted by Culex mosquitoes and reservoir host in this case is birds. It can also be transmitted through contact with other infected animals, their blood, or other tissues. The envelope protein of these viruses is the major source of epitopes and provides protective immunity. Bioinformatics tools were used to identify conserved epitopes in the envelope protein of these viruses. A conserved peptide "TPVGRLVTVNPFV" present in both the viruses containing predicted T and B cell epitopes was found. The model of one of the predicted epitope was generated and upon docking it bound in the groove of HLA-A0201 Class I MHC molecule. Further, it was amenable to proteasomal cleavage enhancing its chances of processing by cytosolic pathway. The peptide was found to be non toxic, non allergenic and stable in mammalian cells based on database search. The population coverage was pan world and nearly 70% identity of the peptide was found in the Zika virus envelope protein. The peptide was located in the domain III of envelope protein which is the exposed domain therefore B cell receptors may recognize this peptide easily. The conserved peptide containing T and B cell epitopes can have future application for designing epitope based vaccines for both JEV and WNV.
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Affiliation(s)
- Parvez Singh Slathia
- School of Biotechnology, Shri Mata Vaishno Devi University, Kakrial, Katra, J&K, India.
| | - Preeti Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Kakrial, Katra, J&K, India
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Pourseif MM, Yousefpour M, Aminianfar M, Moghaddam G, Nematollahi A. A multi-method and structure-based in silico vaccine designing against Echinococcus granulosus through investigating enolase protein. ACTA ACUST UNITED AC 2019; 9:131-144. [PMID: 31508329 PMCID: PMC6726745 DOI: 10.15171/bi.2019.18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/24/2022]
Abstract
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Introduction: Hydatid disease is a ubiquitous parasitic zoonotic disease, which causes different medical, economic and serious public health problems in some parts of the world. The causal organism is a multi-stage parasite named Echinococcus granulosus whose life cycle is dependent on two types of mammalian hosts viz definitive and intermediate hosts.
Methods: In this study, enolase, as a key functional enzyme in the metabolism of E. granulosus (EgEnolase), was targeted through a comprehensive in silico modeling analysis and designing a host-specific multi-epitope vaccine. Three-dimensional (3D) structure of enolase was modeled using MODELLER v9.18 software. The B-cell epitopes (BEs) were predicted based on the multi-method approach and via some authentic online predictors. ClusPro v2.0 server was used for docking-based T-helper epitope prediction. The 3D structure of the vaccine was modeled using the RaptorX server. The designed vaccine was evaluated for its immunogenicity, physicochemical properties, and allergenicity. The codon optimization of the vaccine sequence was performed based on the codon usage table of E. coli K12. Finally, the energy minimization and molecular docking were implemented for simulating the vaccine binding affinity to the TLR-2 and TLR-4 and the complex stability.
Results: The designed multi-epitope vaccine was found to induce anti-EgEnolase immunity which may have the potential to prevent the survival and proliferation of E. granulosus into the definitive host.
Conclusion: Based on the results, this step-by-step immunoinformatics approach could be considered as a rational platform for designing vaccines against such multi-stage parasites. Furthermore, it is proposed that this multi-epitope vaccine is served as a promising preventive anti-echinococcosis agent.
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Affiliation(s)
- Mohammad Mostafa Pourseif
- Department of Physiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran.,Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mitra Yousefpour
- Department of Physiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohammad Aminianfar
- Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Gholamali Moghaddam
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Ahmad Nematollahi
- Department of Pathobiology, Veterinary College, University of Tabriz, Tabriz, Iran
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Khalili S, Rasaee MJ, Mousavi SL, Amani J, Jahangiri A, Borna H. In silico Prediction and in vitro Verification of a Novel Multi-Epitope Antigen for HBV Detection. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2018. [DOI: 10.3103/s0891416817040097] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sefid F, Payandeh Z, Azamirad G, Abdolhamidi R, Rasooli I. In Silico Engineering Towards Enhancement of Bap–VHH Monoclonal Antibody Binding Affinity. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-017-9670-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Jahangiri A, Rasooli I, Owlia P, Imani Fooladi AA, Salimian J. Highly conserved exposed immunogenic peptides of Omp34 against Acinetobacter baumannii: An innovative approach. J Microbiol Methods 2018; 144:79-85. [DOI: 10.1016/j.mimet.2017.11.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 11/16/2022]
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Antigenic Properties of Iron Regulated Proteins in Acinetobacter baumannii: An In Silico Approach. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9665-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Pourseif MM, Moghaddam G, Naghili B, Saeedi N, Parvizpour S, Nematollahi A, Omidi Y. A novel in silico minigene vaccine based on CD4 + T-helper and B-cell epitopes of EG95 isolates for vaccination against cystic echinococcosis. Comput Biol Chem 2017; 72:150-163. [PMID: 29195784 DOI: 10.1016/j.compbiolchem.2017.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/03/2023]
Abstract
EG95 oncospheral antigen plays a crucial role in Echinococcus granulosus pathogenicity. Considering the diversity of antigen among different EG95 isolates, it seems to be an ideal antigen for designing a universal multivalent minigene vaccine, so-called multi-epitope vaccine. This is the first in silico study to design a construct for the development of global EG95-based hydatid vaccine against E. granulosus in intermediate hosts. After antigen sequence selection, the three-dimensional structure of EG95 was modeled and multilaterally validated. The preliminary parameters for B-cell epitope prediction were implemented such as the possible transmembrane helix, signal peptide, post-translational modifications and allergenicity. The high ranked linear and conformational B-cell epitopes derived from several online web-servers (e.g., ElliPro, BepiPred v1.0, BcePred, ABCpred, SVMTrip, IEDB algorithms, SEPPA v2.0 and Discotope v2.0) were utilized for multiple sequence alignment and then for engineering the vaccine construct. T-helper based epitopes were predicted by molecular docking between the high frequent ovar class II allele (Ovar-DRB1*1202) and hexadecamer fragments of the EG95 protein. Having used the immune-informatics tools, we formulated the first EG95-based minigene vaccine based on T-helper epitope with high-binding affinity to the ovar MHC allele. This designed construct was analyzed for different physicochemical properties. It was also codon-optimized for high-level expression in Escherichia coli k12. Taken all, we propose the present in silico vaccine constructs as a promising platform for the generation of broadly protective vaccines for species and genus-specific immunization of the natural hosts of the parasite.
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Affiliation(s)
- Mohammad M Pourseif
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran; Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamali Moghaddam
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Behrouz Naghili
- Research Center for Infectious and Tropical Diseases, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazli Saeedi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Nematollahi
- Department of Pathobiology, Veterinary College, University of Tabriz, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; School of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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In Silico Analyses of Staphylococcal Enterotoxin B as a DNA Vaccine for Cancer Therapy. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9595-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Jahangiri A, Rasooli I, Owlia P, Fooladi AAI, Salimian J. In silico design of an immunogen against Acinetobacter baumannii based on a novel model for native structure of Outer membrane protein A. Microb Pathog 2017; 105:201-210. [DOI: 10.1016/j.micpath.2017.02.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 02/05/2017] [Accepted: 02/20/2017] [Indexed: 11/17/2022]
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Ahmadi A, Farhadi E, Salimian J, Amani J. Designing a vaccine therapy candidate against Propionibacterium acnes: a bioinformatics approach. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2017. [DOI: 10.3103/s0891416816030022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Structural pierce into molecular mechanism underlying Clostridium perfringens Epsilon toxin function. Toxicon 2017; 127:90-99. [PMID: 28089770 DOI: 10.1016/j.toxicon.2017.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/17/2022]
Abstract
Epsilon toxin of the Clostridium perfringens garnered a lot of attention due to its potential for toxicity in humans, extreme potency for cytotoxicity in mice and lack of any approved therapeutics prescribed for human. However, the intricacies of the Epsilon toxin action mechanism are yet to be understood. In this regard, various in silico tools have been exploited to model and refine the 3D structure of the toxin and its two receptors. The receptor proteins were embedded into designed lipid membranes within an aqueous and ionized environment. Thereafter, the modeled structures subjected to series of consecutive molecular dynamics runs to achieve the most natural like coordination for each model. Ultimately, protein-protein interaction analyses were performed to understand the probable action mechanism. The obtained results successfully confirmed the accuracy of employed methods to achieve high quality models for the toxin and its receptors within their lipid bilayers. Molecular dynamics analyses lead the structures to a more native like coordination. Moreover, the results of previous empirical studies were confirmed, while new insights for action mechanisms including the detailed roles of Hepatitis A virus cellular receptor 1 (HAVCR1) and Myelin and lymphocyte protein (MAL) proteins were achieved. In light of previous and our observations, we suggested novel models which elucidated the existing interplay between potential players of Epsilon toxin action mechanism with detailed structural evidences. These models would pave the way to have more robust understanding of the Epsilon toxin biology, more precise vaccine construction and more successful drug (inhibitor) design.
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Khalili S, Mohammadpour H, Shokrollahi Barough M, Kokhaei P. ILP-2 modeling and virtual screening of an FDA-approved library:a possible anticancer therapy. Turk J Med Sci 2016; 46:1135-43. [PMID: 27513416 DOI: 10.3906/sag-1503-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 10/25/2015] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND/AIM The members of the inhibitors of apoptosis protein (IAP) family inhibit diverse components of the caspase signaling pathway, notably caspase 3, 7, and 9. ILP-2 (BIRC-8) is the most recently identified member of the IAPs, mainly interacting with caspase 9. This interaction would eventually lead to death resistance in the case of cancerous cells. Therefore, structural modeling of ILP-2 and finding applicable inhibitors of its interaction with caspase 9 are a compelling challenge. MATERIALS AND METHODS Three main protein modeling approaches along with various model refinement measures were harnessed to achieve a reliable 3D model, using state-of-the-art software. Thereafter, the selected model was employed to perform virtual screening of an FDA approved library. RESULTS A model built by a combinatorial approach (homology and ab initio approaches) was chosen as the best model. Model refinement processes successfully bolstered the model quality. Virtual screening of the compound library introduced several high affinity inhibitor candidates that interact with functional residues of ILP2. CONCLUSION Given the 3D structure of the ILP2 molecule, we found promising inhibitory molecules. In addition to high affinity towards the ILP2 molecule, these molecules interact with residues that play pivotal rules in ILP2-caspase interaction. These molecules would inhibit ILP2-caspase interaction and consequently would lead to reactivated cell apoptosis through the caspases pathway.
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Affiliation(s)
- Saeed Khalili
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hemn Mohammadpour
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Parviz Kokhaei
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK),Karolinska University Hospital Solna and Karolinska Institute, Stockholm, Sweden
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In Silico Sub-unit Hexavalent Peptide Vaccine Against an Staphylococcus aureus Biofilm-Related Infection. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9489-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Khalili S, Rahbar MR, Dezfulian MH, Jahangiri A. In silico analyses of Wilms׳ tumor protein to designing a novel multi-epitope DNA vaccine against cancer. J Theor Biol 2015; 379:66-78. [DOI: 10.1016/j.jtbi.2015.04.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 02/25/2015] [Accepted: 04/20/2015] [Indexed: 02/06/2023]
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Dhama K, Karthik K, Tiwari R, Shabbir MZ, Barbuddhe S, Malik SVS, Singh RK. Listeriosis in animals, its public health significance (food-borne zoonosis) and advances in diagnosis and control: a comprehensive review. Vet Q 2015; 35:211-35. [PMID: 26073265 DOI: 10.1080/01652176.2015.1063023] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Listeriosis is an infectious and fatal disease of animals, birds, fish, crustaceans and humans. It is an important food-borne zoonosis caused by Listeria monocytogenes, an intracellular pathogen with unique potential to spread from cell to cell, thereby crossing blood-brain, intestinal and placental barriers. The organism possesses a pile of virulence factors that help to infect the host and evade from host immune machinery. Though disease occurrence is sporadic throughout the world, it can result in severe damage during an outbreak. Listeriosis is characterized by septicaemia, encephalitis, meningitis, meningoencephalitis, abortion, stillbirth, perinatal infections and gastroenteritis with the incubation period varying with the form of infection. L. monocytogenes has been isolated worldwide from humans, animals, poultry, environmental sources like soil, river, decaying plants, and food sources like milk, meat and their products, seafood and vegetables. Since appropriate vaccines are not available and infection is mainly transmitted through foods in humans and animals, hygienic practices can prevent its spread. The present review describes etiology, epidemiology, transmission, clinical signs, post-mortem lesions, pathogenesis, public health significance, and advances in diagnosis, vaccines and treatment of this disease. Special attention has been given to novel as well as prospective emerging therapies that include bacteriophage and cytokine therapy, avian egg yolk antibodies and herbal therapy. Various vaccines, including advances in recombinant and DNA vaccines and their modes of eliciting immune response, are also discussed. Due focus has also been given regarding appropriate prevention and control strategies to be adapted for better management of this zoonotic disease.
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Affiliation(s)
- Kuldeep Dhama
- a Division of Pathology , Indian Veterinary Research Institute (IVRI) , Izatnagar, Bareilly 243122 , UP , India
| | - Kumaragurubaran Karthik
- b Division of Bacteriology and Mycology , Indian Veterinary Research Institute (IVRI) , Izatnagar, Bareilly 243122 , UP , India
| | - Ruchi Tiwari
- c Department of Veterinary Microbiology and Immunology , College of Veterinary Sciences , Uttar Pradesh Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura 281001 , India
| | - Muhammad Zubair Shabbir
- d Quality Operations Laboratory , University of Veterinary and Animal Sciences , Lahore 54600, Pakistan
| | - Sukhadeo Barbuddhe
- e Indian Council of Agricultural Research Complex for Goa , Old Goa, Goa 403402, India
| | - Satya Veer Singh Malik
- f Division of Veterinary Public Health , Indian Veterinary Research Institute (IVRI) , Izatnagar, Bareilly 243122 , UP , India
| | - Raj Kumar Singh
- g Indian Veterinary Research Institute (IVRI) , Izatnagar, Bareilly 243122 , UP , India
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Sefid F, Rasooli I, Jahangiri A, Bazmara H. Functional Exposed Amino Acids of BauA as Potential Immunogen Against Acinetobacter baumannii. Acta Biotheor 2015; 63:129-49. [PMID: 25840681 DOI: 10.1007/s10441-015-9251-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 03/31/2015] [Indexed: 12/12/2022]
Abstract
Multidrug-resistant Acinetobacter baumannii is recognized to be among the most difficult antimicrobial-resistant gram negative bacilli to control and treat. One of the major challenges that the pathogenic bacteria face in their host is the scarcity of freely available iron. To survive under such conditions, bacteria express new proteins on their outer membrane and also secrete iron chelators called siderophores. Antibodies directed against these proteins associated with iron uptake exert a bacteriostatic or bactericidal effect against A. baumanii in vitro, by blocking siderophore mediated iron uptake pathways. Attempts should be made to discover peptides that could mimic protein epitopes and possess the same immunogenicity as the whole protein. Subsequently, theoretical methods for epitope prediction have been developed leading to synthesis of such peptides that are important for development of immunodiagnostic tests and vaccines. The present study was designed to in silico resolving the major obstacles in the control or in prevention of the diseases caused by A. baumannii. We exploited bioinformatic tools to better understand and characterize the Baumannii acinetobactin utilization structure of A. baumannii and select appropriate regions as effective B cell epitopes. In conclusion, amino acids 26-191 of cork domain and 321-635 of part of the barrel domain including L4-L9, were selected as vaccine candidates. These two regions contain functional exposed amino acids with higher score of B cell epitopes properties. Majority of amino acids are hydrophilic, flexible, accessible, and favorable for B cells from secondary structure point of view.
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Affiliation(s)
- Fatemeh Sefid
- Department of Biology, Shahed University, Tehran-Qom Express Way, Opposite Imam Khomeini's Shrine, 3319118651, Tehran, Iran
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22
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Khalili S, Jahangiri A, Borna H, Ahmadi Zanoos K, Amani J. Computational vaccinology and epitope vaccine design by immunoinformatics. Acta Microbiol Immunol Hung 2014; 61:285-307. [PMID: 25261943 DOI: 10.1556/amicr.61.2014.3.4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Human immune system includes variety of different cells and molecules correlating with other body systems. These instances complicate the analysis of the system; particularly in postgenomic era by introducing more amount of data, the complexity is increased and necessity of using computational approaches to process and interpret them is more tangible.Immunoinformatics as a subset of bioinformatics is a new approach with variety of tools and databases that facilitate analysis of enormous amount of immunologic data obtained from experimental researches. In addition to directing the insight regarding experiment selections, it helps new thesis design which was not feasible with conventional methods due to the complexity of data. Considering this features immunoinformatics appears to be one of the fields that accelerate the immunological research progression.In this study we discuss advances in genomics and vaccine design and their relevance to the development of effective vaccines furthermore several division of this field and available tools in each item are introduced.
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Affiliation(s)
- Saeed Khalili
- 1 Tarbiat Modares University Department of Medical Biotechnology Tehran Iran
| | - Abolfazl Jahangiri
- 2 Baqiyatallah University of Medical Sciences Applied Microbiology Research Center Tehran Iran
| | - Hojat Borna
- 3 Baqiyatallah Medical Science University Chemical Injuries Research Center Tehran Iran
| | | | - Jafar Amani
- 2 Baqiyatallah University of Medical Sciences Applied Microbiology Research Center Tehran Iran
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23
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In silico determination and validation of baumannii acinetobactin utilization a structure and ligand binding site. BIOMED RESEARCH INTERNATIONAL 2013; 2013:172784. [PMID: 24106696 PMCID: PMC3780550 DOI: 10.1155/2013/172784] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/21/2013] [Accepted: 07/31/2013] [Indexed: 01/21/2023]
Abstract
Acinetobacter baumannii is a deadly nosocomial pathogen. Iron is an essential element for the pathogen. Under iron-restricted conditions, the bacterium expresses iron-regulated outer membrane proteins (IROMPs). Baumannii acinetobactin utilization (BauA) is the most important member of IROMPs in A. baumannii. Determination of its tertiary structure could help deduction of its functions and its interactions with ligands. The present study unveils BauA 3D structure via in silico approaches. Apart from ab initio, other rational methods such as homology modeling and threading were invoked to achieve the purpose. For homology modeling, BLAST was run on the sequence in order to find the best template. The template was then served to model the 3D structure. All the models built were evaluated qualitatively. The best model predicted by LOMETS was selected for analyses. Refinement of 3D structure as well as determination of its clefts and ligand binding sites was carried out on the structure. In contrast to the typical trimeric arrangement found in porins, BauA is monomeric. The barrel is formed by 22 antiparallel transmembrane β -strands. There are short periplasmic turns and longer surface-located loops. An N-terminal domain referred to either as the cork, the plug, or the hatch domain occludes the β -barrel.
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24
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Toobak H, Rasooli I, Talei D, Jahangiri A, Owlia P, Darvish Alipour Astaneh S. Immune response variations to Salmonella enterica serovar Typhi recombinant porin proteins in mice. Biologicals 2013; 41:224-30. [PMID: 23796754 DOI: 10.1016/j.biologicals.2013.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 05/14/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVES Typhoid fever is caused by Salmonella enterica serovar Typhi. OmpC, OmpF and OmpA, the three major outer membrane proteins (OMPs), could serve as vaccine candidates. METHODS The porins antigenicity was predicted in silico. The OMP genes were amplified, cloned and expressed. Sero-reactivities of the recombinant proteins purified by denaturing method were assayed by ELISA. BALB/c mice were immunized with the recombinant porins followed by bacterial challenge. RESULTS Bacterial challenge of the animal model brought about antibody triggering efficacy of the antigen in OmpF > OmpC > OmpA order. Experimental findings validated the in silico results. None of the antigens had synergic or antagonistic effects on each other from immune system induction points of view. Despite their high immunogenicity, none of the antigens was protective. However, administration of two or three antigens simultaneously resulted in retardation of lethal effect. Porins, in addition to their specific functions, share common functions. Hence, they can compensate for each other's functions. CONCLUSIONS The produced antibodies could not eliminate the pathogenicity by blockade of one or some of the antigens. Porin antigens are not suitable vaccine candidates alone or in denatured forms. Native forms of the antigens maybe studied for protective immunogenicity.
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Affiliation(s)
- Hoda Toobak
- Department of Biology, Shahed University, Tehran-Qom Express Way, Opposite Imam Khomeini's Shrine, Tehran 3319118651, Iran
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Jahangiri A, Rasooli I, Reza Rahbar M, Khalili S, Amani J, Ahmadi Zanoos K. Precise detection of L. monocytogenes hitting its highly conserved region possessing several specific antibody binding sites. J Theor Biol 2012; 305:15-23. [DOI: 10.1016/j.jtbi.2012.04.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 04/07/2012] [Accepted: 04/09/2012] [Indexed: 12/23/2022]
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26
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Rai J, Lok KI, Mok CY, Mann H, Noor M, Patel P, Flower DR. Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates: E coli 536. Bioinformation 2012; 8:272-5. [PMID: 22493535 PMCID: PMC3321237 DOI: 10.6026/97320630008272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 03/28/2012] [Indexed: 11/24/2022] Open
Abstract
Epitope prediction is becoming a key tool for vaccine discovery. Prospective analysis of bacterial and viral genomes can identify antigenic epitopes encoded within individual genes that may act as effective vaccines against specific pathogens. Since B-cell epitope prediction remains unreliable, we concentrate on T-cell epitopes, peptides which bind with high affinity to Major Histacompatibility Complexes (MHC). In this report, we evaluate the veracity of identified T-cell epitope ensembles, as generated by a cascade of predictive algorithms (SignalP, Vaxijen, MHCPred, IDEB, EpiJen), as a candidate vaccine against the model pathogen uropathogenic gram negative bacteria Escherichia coli (E-coli) strain 536 (O6:K15:H31). An immunoinformatic approach was used to identify 23 epitopes within the E-coli proteome. These epitopes constitute the most promiscuous antigenic sequences that bind across more than one HLA allele with high affinity (IC50 < 50nM). The reliability of software programmes used, polymorphic nature of genes encoding MHC and what this means for population coverage of this potential vaccine are discussed.
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Affiliation(s)
- Jade Rai
- Aston Pharmacy School, Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Ka In Lok
- Aston Pharmacy School, Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Chun Yin Mok
- Aston Pharmacy School, Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Harvinder Mann
- Aston Pharmacy School, Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Mohammed Noor
- Aston Pharmacy School, Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Pritesh Patel
- Aston Pharmacy School, Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Darren R Flower
- Aston Pharmacy School, Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
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Rahbar MR, Rasooli I, Gargari SLM, Sandstrom G, Amani J, Fattahian Y, Jahangiri A, Jalali M. A potential in silico antibody–antigen based diagnostic test for precise identification of Acinetobacter baumannii. J Theor Biol 2012; 294:29-39. [DOI: 10.1016/j.jtbi.2011.10.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/07/2011] [Accepted: 10/18/2011] [Indexed: 10/15/2022]
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