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Khan K, Jalal K, Uddin R. An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58. Genomics 2022; 114:110301. [PMID: 35149170 DOI: 10.1016/j.ygeno.2022.110301] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 12/25/2021] [Accepted: 02/01/2022] [Indexed: 12/14/2022]
Abstract
Salmonella typhi is notorious for causing enteric fever which is also known as typhoid fever. It emerged as an extreme drug resistant strain that requires urgent attention to prevent its global spread. Statistically, about 11-17 million typhoid illnesses are reported worldwide annually. The only alternative approach for the control of this illness is proper vaccination. However, available typhoid vaccine has certain limitations such as poor long-term efficacy, and non-recommendation for below 6 years children, which opens the avenues for designing new vaccines to overcome such limitations. Computational-based reverse vaccinology along with subtractive genomics analysis is one of the robust approaches used for the prioritization of vaccine candidates through direct screening of genome sequence assemblies. In the current study, we have successfully designed a peptide-based novel antigen chimeric vaccine candidate against the XDR strain of S. typhi H58. The pipeline revealed four peptides from WP_001176621.1 i.e., peptidoglycan-associated lipoprotein Pal and two peptides from WP_000747548.1 i.e., OmpA family lipoprotein as promising target for the induction of immune response against S. typhi. The six epitopes from both proteins were found as immunogenic, antigenic, virulent, highly conserved, nontoxic, and non-allergenic among whole Salmonella H58 proteome. Furthermore, the binding interaction between a chimeric vaccine and human population alleles was unveiled through structure-based studies. So far, these proteins have never been characterized as vaccine targets against S. typhi. The current study proposed that construct V2 could be a significant vaccine candidate against S. typhi H58. However, to ascertain this, future experimental holistic studies are recommended as follow-up.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
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Design of a peptide-based vaccine from late stage specific immunogenic cross-reactive antigens of PE/PPE proteins of Mycobacterium tuberculosis. Eur J Pharm Sci 2021; 168:106051. [PMID: 34744006 DOI: 10.1016/j.ejps.2021.106051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/25/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
Since decades now, Tuberculosis (TB) is among the leading cause of death globally. Innovative and extensive research strategies are necessary to lower TB incidence and achieve the End TB Strategy milestone. Epitope-based vaccine designing and development provides a promising solution with high efficacy and effectiveness. Mining of less studied genes of Mycobacterium tuberculosis (Mtb) is crucial for recognizing potential antigenic peptide epitopes which can mount protective immune response in host. Many proteins from ESX associated Proline-Glutamate (PE)/ Proline-Proline-Glutamate (PPE) family are virulence factors and alter host mediated immune response against the pathogen. In the present study, we have targeted 34 late stage expressing (being expressed at 90 days) PE/PPE proteins of Mtb for prediction and identification of promiscuous, immunogenic and cross-reactive CD4+ T cell specific epitopes. We found a total of 149 promiscuous and cross-reactive epitopes out of which 42 were antigenic as well. Further, we shortlisted top 10 Promiscuous, Cross-reactive CD4+ T cell specific, Antigenic Peptide Epitopes (PCAPEs) which were characterized to be non-allergenic and pro-inflammatory cytokine inducing in nature. These epitopes also showed strong binding affinity for CD8+ T cell restricted Major Histo-compatibility Complex (MHC) class I alleles. Additionally, these PCAPEs showed wide population coverage of 99.6% globally for both MHC class I and class II alleles. Molecular docking studies were conducted to confirm the affinity of these shortlisted peptides for widely occurring MHC alleles. Additionally, we performed codon adaptation and in silico cloning of the recombinant vaccine construct incorporating EsxA (ESAT-6) as an adjuvant and the 10 selected PCAPEs joined by linkers. The recombinant vaccine construct showed strong affinity for Toll-like receptor2 (TLR2) immune receptor in docking studies. In silico prediction based study using C-ImmSim server shows significant population of Th1 type immune cells with memory cells lasting for months in response to our vaccine administration. Since, majority of TB vaccines under clinical trials are antigens expressed at early stages; a combinatorial approach inclusive of peptide epitopes derived from proteins being expressed at all stages could be a promising strategy to design and develop effective TB vaccine. Synthesis and experimental validation of this multi-epitopic recombinant TB vaccine construct may result in an effective vaccine to confer protection against Mtb.
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Madan R, Pandit K, Bhati L, Kumar H, Kumari N, Singh S. Mining the Mycobacterium tuberculosis proteome for identification of potential T-cell epitope based vaccine candidates. Microb Pathog 2021; 157:104996. [PMID: 34044044 DOI: 10.1016/j.micpath.2021.104996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/22/2022]
Abstract
Identification of protective antigens for designing a high-efficacy tuberculosis vaccine is the need of the hour. Till date only 7% of the Mycobacterium tuberculosis proteome has been explored for discovering antigens capable of activating T-cell responses. Therefore, it becomes crucial to screen the remaining Mycobacterium tuberculosis proteome for more immunodominant T-cell epitopes. An extensive knowledge of the epitopes recognized by our immune system can aid this process of finding potential T cell antigens for development of a better TB vaccine. In the present in-silico study, 237 proteins belonging to the 'virulence, detoxification, and adaptation' category of Mycobacterium tuberculosis proteome were targeted for T-cell epitope screening. 50825 MHC Class I and 49357 MHC Class II epitopes were generated using NetMHC3.4 and IEDB servers respectively and tested for their antigenicity and cytokine stimulation. The highest antigenic epitopes were analyzed for their world population coverage and epitope conservancy. Molecular docking and molecular dynamics simulation studies were performed to corroborate the binding affinities and structural stability of the peptide-MHC complexes. We predicted a total of 3 MHC Class I (ILLKMCWPA, FAVGMNVYV, and SLAGNSAKV) and 7 MHC Class II (DLTIGFFLHIPFPPV, RPDLTIGFFLHIPFP, LTIGFFLHIPFPPVE, VLVFALVVALVYLQF, LVFALVVALVYLQFR, PNLVAARFIQLTPVY, and LVLVFALVVALVYLQ) epitopes that can be promising vaccine candidates. These predicted epitopes belong to 6 distinct proteins: Rv0169 (mce1a), Rv3490 (ostA), Rv3496 (mce4D), Rv1085c, Rv0563 (HtpX), Rv3497c (mce4C). All these proteins are expressed at different stages in the life cycle of Mycobacterium tuberculosis and thus, the predicted epitopes could be employed as candidates for designing a multistage-multiepitopic vaccine.
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Affiliation(s)
- Riya Madan
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Kushankur Pandit
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Lavi Bhati
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Hindesh Kumar
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Neha Kumari
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Swati Singh
- Department of Zoology, Hansraj College, University of Delhi, India.
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Designing a conserved peptide-based subunit vaccine against SARS-CoV-2 using immunoinformatics approach. In Silico Pharmacol 2021; 9:8. [PMID: 33425647 PMCID: PMC7785481 DOI: 10.1007/s40203-020-00062-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
The widespread of coronavirus (COVID-19) is a new global health crisis that poses a threat to the world. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in bats and was discovered first in Wuhan, Hubei province, China in December 2019. Immunoinformatics and bioinformatics tools were employed for the construction of a multi-epitope subunit vaccine to prevent the diseases. The antigenicity, toxicity and allergenicity of all epitopes used in the construction of the vaccine were predicted and then conjugated with adjuvants and linkers. Vaccine Toll-Like Receptors (2, 3, 4, 8 and 9) complex was also evaluated. The vaccine construct was antigenic, non-toxic and non-allergic, which indicates the vaccines ability to induce antibodies in the host, making it an effective vaccine candidate. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-020-00062-x.
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Oladipo EK, Ajayi AF, Ariyo OE, Onile SO, Jimah EM, Ezediuno LO, Adebayo OI, Adebayo ET, Odeyemi AN, Oyeleke MO, Oyewole MP, Oguntomi AS, Akindiya OE, Olamoyegun BO, Aremu VO, Arowosaye AO, Aboderin DO, Bello HB, Senbadejo TY, Awoyelu EH, Oladipo AA, Oladipo BB, Ajayi LO, Majolagbe ON, Oyawoye OM, Oloke JK. Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19. INFORMATICS IN MEDICINE UNLOCKED 2020; 21:100438. [PMID: 33043110 PMCID: PMC7533051 DOI: 10.1016/j.imu.2020.100438] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 09/27/2020] [Indexed: 01/07/2023] Open
Abstract
Stimulation and generation of T and B cell-mediated long-term immune response are essential for the curbing of a deadly virus such as SAR-CoV-2 (Severe Acute Respiratory Corona Virus 2). Immunoinformatics approach in vaccine design takes advantage of antigenic and non-allergenic epitopes present on the spike glycoprotein of SARS-CoV-2 to elicit immune responses. T cells and B cells epitopes were predicted, and the selected residues were subjected to allergenicity, antigenicity and toxicity screening which were linked by appropriate linkers to form a multi-epitope subunit vaccine. The physiochemical properties of the vaccine construct were analyzed, and the molecular weight, molecular formula, theoretical isoelectric point value, half-life, solubility score, instability index, aliphatic index and GRAVY were predicted. The vaccine structure was constructed, refined, validated, and disulfide engineered to get the best model. Molecular binding simulation and molecular dynamics simulation were carried out to predict the stability and binding affinity of the vaccine construct with TLRs. Codon acclimatization and in silico cloning were performed to confirm the vaccine expression and potency. Results obtained indicated that this novel vaccine candidate is non-toxic, capable of initiating the immunogenic response and will not induce an allergic reaction. The highest binding energy was observed in TLR4 (Toll-like Receptor 4) (−1398.1), and the least is TLR 2 (−1479.6). The steady rise in Th (T-helper) cell population with memory development was noticed, and IFN-g (Interferon gamma) was provoked after simulation. At this point, the vaccine candidate awaits animal trial to validate its efficacy and safety for use in the prevention of the novel COVID-19 (Coronavirus Disease 2019) infections.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Ayodeji Folorunsho Ajayi
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olumuyiwa Elijah Ariyo
- Department of Medicine, Infectious Diseases and Tropical Medicine Unit, Federal Teaching Hospital, Ido-Ekiti, Ekiti State, Nigeria
| | | | - Esther Moradeyo Jimah
- Department of Medical Microbiology and Parasitology, University of Ilorin, Kwara State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Louis Odinakaose Ezediuno
- Department of Microbiology and Parasitology, University of Ilorin, Kwara State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Oluwadunsin Iyanuoluwa Adebayo
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Emmanuel Tayo Adebayo
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Aduragbemi Noah Odeyemi
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Marvellous Oluwaseun Oyeleke
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | | | - Olawumi Elizabeth Akindiya
- Microbiology Programme, Department of Biological Science, Olusegun Agagu University of Science and Technology, Okitipupa, Ondo State, Nigeria
| | | | - Victoria Oyetayo Aremu
- Reproduction and Bioinformatics Unit, Department of Medical Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Consult, Ogbomoso, Oyo state, Nigeria
| | - Abiola O Arowosaye
- Department of Virology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | | | | | - Elukunbi Hilda Awoyelu
- Department of Natural Sciences, Precious Conerstone University, Ibadan, Oyo State, Nigeria
| | - Adio Abayomi Oladipo
- Department of Haematology and Blood Grouping Serology, Obafemi Awolowo Teaching Hospital Complex, Ile-Ife Wesley Guild Hospital Wing, Osun State, Nigeria
| | - Bukola Bisola Oladipo
- Department of Clinical Nursing, Bowen University Teaching Hospital, Ogbomoso, Oyo State, Nigeria
| | | | - Olusola Nathaniel Majolagbe
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olubukola Monisola Oyawoye
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Julius Kola Oloke
- Department of Natural Sciences, Precious Conerstone University, Ibadan, Oyo State, Nigeria
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Singh M, Bhatt P, Sharma M, Varma-Basil M, Chaudhry A, Sharma S. Immunogenicity of late stage specific peptide antigens of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2019; 74:103930. [PMID: 31228643 DOI: 10.1016/j.meegid.2019.103930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/06/2019] [Accepted: 06/18/2019] [Indexed: 01/05/2023]
Abstract
Global burden of latent TB infection comprises one-third of the world population. Identifying potential Mycobacterium tuberculosis (Mtb) latency associated antigens that can generate protective immunity against the pathogen is crucial for designing an effective TB vaccine. Usually the immune system responds to a small number of amino acids as MHC Class I or Class II peptides. The precision to trigger epitope specific protective T-cell immune response could therefore be achieved with synthetic peptide-based subunit vaccine. In the present study we have considered an immunoinformatic approach using available softwares (ProPred, IEDB, NETMHC, BIMAS, Vaxijen2.0) and docking and visualizing softwares (CABSDOCK, HEX, Pymol, Discovery Studio) to select 10 peptides as latency antigens from 4 proteins (Rv2626, Rv2627, Rv2628, and Rv2032) of DosR regulon of Mtb. As Intracellular IFN-γ secreted by T cells is the most essential cytokine in Th1 mediated protective immunity, these peptides were verified as potential immunogenic epitopes in Peripheral Blood Mononuclear Cells (PBMCs) of 10 healthy contacts of TB patients (HTB) and 10 Category I Pulmonary TB patients (PTB).The antigen-specific CD4 and CD8 T cells expressing intracellular IFN-γ were analyzed using monoclonal antibodies in all subjects by multi-parameter flow cytometry. Both, PTB and HTB individuals responded to DosR peptides by showing increased frequency of IFN-γ+CD4 and IFN-γ+CD8 T cells. The T-cell responses were significantly higher in PTB patients in comparision to the HTB individuals. Additionally, our synthetic peptides and pools showed higher frequencies of IFN-γ+CD4 and IFN-γ+CD8 T cells than the peptides of Ag85B. This pilot study can be taken up further in larger sample size which may support the untapped opportunity of designing Mtb DosR inclusive peptide based post-exposure subunit vaccine.
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Affiliation(s)
- Medha Singh
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | - Parul Bhatt
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | | | - Anil Chaudhry
- Rajan Babu Institute of Pulmonary Medicine and Tuberculosis Hospital, GTB Nagar, Delhi 110009, India
| | - Sadhna Sharma
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
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Rv2626c and Rv2032 activate TH1 response and downregulate regulatory T cells in peripheral blood mononuclear cells of tuberculosis patients. Comp Immunol Microbiol Infect Dis 2019; 62:46-53. [DOI: 10.1016/j.cimid.2018.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/24/2018] [Accepted: 11/27/2018] [Indexed: 12/19/2022]
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Pandey K, Singh S, Bhatt P, Medha, Sharma M, Chaudhry A, Sharma S. DosR proteins of Mycobacterium tuberculosis upregulate effector T cells and down regulate T regulatory cells in TB patients and their healthy contacts. Microb Pathog 2018; 126:399-406. [PMID: 30476579 DOI: 10.1016/j.micpath.2018.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
Abstract
It is well established that the current problem of tuberculosis (TB) can be combated by overcoming the drawbacks of the currently available BCG vaccine. This would involve incorporation of antigens that can control TB at all stages including the dormant phase which is generally ignored. Hence, DosR regulon proteins, which are expressed in latent infection, could prove to be very good vaccine candidates as they can possibly target the silent but most predominant form of TB infection. In the present study, the immune response to two DosR proteins Rv2627 and Rv2628 has been studied in PBMCs derived from normal individuals, TB patients and healthy contacts of TB patients. It was found that these antigens were capable of stimulating a strong IFN-γ+ T cell response along with accentuation of memory T cells and other protective cytokines such as IL-2 and IL-17. At the same time these proteins decreased the frequencies of immune-suppressor regulatory T cells in in vitro stimulation of PBMC from both patients and their contacts. Considering all these facts together, we suggest Rv2627 and Rv2628 to be one of the extremely promising candidates for incorporation into a post exposure subunit vaccine against TB.
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Affiliation(s)
- Kirti Pandey
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House, and Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India.
| | - Swati Singh
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House, and Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India.
| | - Parul Bhatt
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House, and Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India.
| | - Medha
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House, and Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India.
| | - Monika Sharma
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House, and Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India.
| | - Anil Chaudhry
- Rajan Babu Institute of Pulmonary Medicine and Tuberculosis Hospital, GTB Nagar, Delhi, 110009, India.
| | - Sadhna Sharma
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House, and Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India.
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Bragazzi NL, Gianfredi V, Villarini M, Rosselli R, Nasr A, Hussein A, Martini M, Behzadifar M. Vaccines Meet Big Data: State-of-the-Art and Future Prospects. From the Classical 3Is ("Isolate-Inactivate-Inject") Vaccinology 1.0 to Vaccinology 3.0, Vaccinomics, and Beyond: A Historical Overview. Front Public Health 2018; 6:62. [PMID: 29556492 PMCID: PMC5845111 DOI: 10.3389/fpubh.2018.00062] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/16/2018] [Indexed: 12/20/2022] Open
Abstract
Vaccines are public health interventions aimed at preventing infections-related mortality, morbidity, and disability. While vaccines have been successfully designed for those infectious diseases preventable by preexisting neutralizing specific antibodies, for other communicable diseases, additional immunological mechanisms should be elicited to achieve a full protection. “New vaccines” are particularly urgent in the nowadays society, in which economic growth, globalization, and immigration are leading to the emergence/reemergence of old and new infectious agents at the animal–human interface. Conventional vaccinology (the so-called “vaccinology 1.0”) was officially born in 1796 thanks to the contribution of Edward Jenner. Entering the twenty-first century, vaccinology has shifted from a classical discipline in which serendipity and the Pasteurian principle of the three Is (isolate, inactivate, and inject) played a major role to a science, characterized by a rational design and plan (“vaccinology 3.0”). This shift has been possible thanks to Big Data, characterized by different dimensions, such as high volume, velocity, and variety of data. Big Data sources include new cutting-edge, high-throughput technologies, electronic registries, social media, and social networks, among others. The current mini-review aims at exploring the potential roles as well as pitfalls and challenges of Big Data in shaping the future vaccinology, moving toward a tailored and personalized vaccine design and administration.
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Affiliation(s)
- Nicola Luigi Bragazzi
- Department of Health Sciences (DISSAL), School of Public Health, University of Genoa, Genoa, Italy
| | - Vincenza Gianfredi
- Department of Experimental Medicine, Unit of Public Health, School of Specialization in Hygiene and Preventive Medicine, University of Perugia, Perugia, Italy
| | - Milena Villarini
- Unit of Public Health, Department of Pharmaceutical Science, University of Perugia, Perugia, Italy
| | | | - Ahmed Nasr
- Department of Medicine and Surgery, Pathology University Milan Bicocca, San Gerardo Hospital, Monza, Italy
| | - Amr Hussein
- Medical Faculty, University of Parma, Parma, Italy
| | - Mariano Martini
- Section of History of Medicine and Ethics, Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Masoud Behzadifar
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
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de Souza C, Lopes MD, De Oliveira FM, Passos MJF, Ferreira LCG, Faria BF, Villar JAFP, Junior MC, Taranto AG, Dos Santos LL, Fonseca CT, de Oliveira Lopes D. Rational selection of immunodominant and preserved epitope Sm043300e from Schistosoma mansoni and design of a chimeric molecule for biotechnological purposes. Mol Immunol 2017; 93:133-143. [PMID: 29175593 DOI: 10.1016/j.molimm.2017.11.019] [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: 08/09/2017] [Revised: 11/12/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022]
Abstract
Human schistosomiasis is a neglected tropical disease of great importance in public health. A large number of people are infected with schistosomiasis, making vaccine development and effective diagnosis important control strategies. A rational epitope prediction workflow using Schistosoma mansoni hypothetical proteins was previously presented by our group, and an improvement to that approach is presented here. Briefly, immunodominant epitopes from parasite membrane proteins were predicted by reverse vaccinology strategy with additional in silico analysis. Furthermore, epitope recognition was evaluated using sera of individuals infected with S. mansoni. The epitope that stood out in both in silico and in vitro assays was used to compose a rational chimeric molecule to improve immune response activation. Out of 2185 transmembrane proteins, four epitopes with high binding affinities for human and mouse MHCII molecules were selected through computational screening. These epitopes were synthesized to evaluate their ability to induce TCD4+ lymphocyte proliferation in mice. Sm204830e and Sm043300e induced significant TCD4+ proliferation. Both epitopes were submitted to enzyme-linked immunosorbent assay to evaluate their recognition by IgG antibodies from the sera of infected individuals, and epitope Sm043300 was significantly recognized in most sera samples. Epitope Sm043300 also showed good affinity for human MHCII molecules in molecular docking, and its sequence is curiously highly conserved in four S. mansoni proteins, all of which are described as G-protein-coupled receptors. In addition, we have demonstrated the feasibility of incorporating this epitope, which showed low similarity to human sequences, into a chimeric molecule. The stability of the molecule was evaluated by molecular modeling aimed at future molecule production for use in diagnosis and vaccination trials.
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Affiliation(s)
- Cláudia de Souza
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil; Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Marcelo Donizete Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil; Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Flávio Martins De Oliveira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil
| | - Maria Juliana Ferreira Passos
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil; Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Laís Cunha Grossi Ferreira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil
| | - Bruna Franciele Faria
- Laboratório de Modelagem Molecular, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | | | - Moacyr Comar Junior
- Laboratório de Modelagem Molecular, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Alex Guterres Taranto
- Laboratório de Modelagem Molecular, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Luciana Lara Dos Santos
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil
| | - Cristina Toscano Fonseca
- Grupo de Pesquisa em Biologia e Imunologia de doenças Infeciosas e Parasitária, Centro de Pesquisas René Rachou-Fundação Oswaldo Cruz, Av. Augusto de Lima, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Débora de Oliveira Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil.
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María RR, Arturo CJ, Alicia JA, Paulina MG, Gerardo AO. The Impact of Bioinformatics on Vaccine Design and Development. Vaccines (Basel) 2017. [DOI: 10.5772/intechopen.69273] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Predicting promiscuous antigenic T cell epitopes of Mycobacterium tuberculosis mymA operon proteins binding to MHC Class I and Class II molecules. INFECTION GENETICS AND EVOLUTION 2016; 44:182-189. [DOI: 10.1016/j.meegid.2016.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/24/2016] [Accepted: 07/03/2016] [Indexed: 11/21/2022]
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