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In silico vaccine

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https://www.readbyqxmd.com/read/28588634/in-silico-identification-of-epitopes-from-house-cat-and-dog-proteins-as-peptide-immunotherapy-candidates-based-on-human-leukocyte-antigen-binding-affinity
#1
H N Tipu, D Ahmed, S A H Gardezi
The objective of this descriptive study was to determine Felis domesticus (cat) and Canis familiaris (dog) protein epitopes that bind strongly to selected HLA class II alleles to identify synthetic vaccine candidate epitopes and to identify individuals/populations who are likely to respond to vaccines. FASTA amino acid sequences of experimentally validated allergenic proteins of house cat and dog were identified using International Union of Immunological Societies (IUIS) allergen nomenclature database. NetMHCII 2...
2017: Iranian journal of veterinary research
https://www.readbyqxmd.com/read/28584981/immunoinformatics-as-a-tool-for-new-antifungal-vaccines
#2
Rupanjali Chaudhuri, Srinivasan Ramachandran
Immunoinformatics aids in screening for vaccine candidates, which can be experimentally tested for their efficacy. This chapter describes methods to use immunoinformatics to screen fungal vaccines candidates. Surface-localized molecules called adhesins could elicit immune response and serve as efficient vaccine candidates. The screening process is patterned on two steps, namely, a First Layer screen mostly used for value addition and prioritization based on characteristics of known antigens and a Second Layer highly focussed on core immunoinformatics analysis involving the binding and interactions of the molecules of the immune system...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28570984/in-silico-identification-of-vaccine-candidates-against-klebsiella-oxytoca
#3
Sandipan Talukdar, Udeshna Bayan, Kandarpa Kr Saikia
Klebsiella oxytoca causes several diseases in immunocompromised as well as healthy individuals. Increasing resistance to a number of antibiotics makes treatment options limited. Prevention using vaccine could be an important solution to get rid of infections caused by Klebsiella oxytoca. In recent time, genome based approaches have contributed significantly in vaccine development. Our aim was to identify the most conserved and immunogenic antigens that can be considered as potential vaccine candidates. KEGG database was used to find out pathways unique to the bacteria...
May 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28560699/identification-of-strategic-residues-at-the-interface-of-antigen-antibody-interactions-by-in-silico-mutagenesis
#4
Lu Xin, Hai Yu, Qiyang Hong, Xingjian Bi, Xiao Zhang, Zhiqing Zhang, Zhibo Kong, Qingbing Zheng, Ying Gu, Qinjian Zhao, Jun Zhang, Shaowei Li, Ningshao Xia
Structural information pertaining to antigen-antibody interactions is fundamental in immunology, and benefits structure-based vaccine design. Modeling of antigen-antibody immune complexes from co-crystal structures or molecular docking simulations provides an extensive profile of the epitope at the interface; however, the key amino acids involved in the interaction must be further clarified, often through the use of experimental mutagenesis and subsequent binding assays. Here, we describe an in silico mutagenesis method to identify key sites at antigen-antibody interfaces, using significant increase in pH-dependency energy among saturated point mutations...
May 30, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28558204/development-and-application-of-synthetic-affinity-ligands-for-the-purification-of-ferritin-based-influenza-antigens
#5
Shaleem I Jacob, Basmah Khogeer, Nick Bampos, Tom Sheppard, Richard Schwartz, Christopher R Lowe
A recently developed novel recombinant influenza antigen vaccine has shown great success in preclinical studies in ferrets and mice. It provides broader protection, and is efficient to manufacture compared to the conventional trivalent influenza vaccines (TIV). Each strain of the recombinant antigen has a constant self-assembled bacterial ferritin core which, if used as a target for affinity chromatography, could lead to a universal purification method. Ferritin in silico models were used to explore potential target binding sites against ligands synthesized by the four-component Ugi reaction...
June 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28555545/identification-of-cross-reacting-t-cell-epitopes-in-structural-and-non-structural-proteins-of-swine-and-pandemic-h1n1-influenza-a-virus-strains-in-pigs
#6
Massimiliano Baratelli, Lasse Eggers Pedersen, Ramona Trebbien, Lars Erik Larsen, Gregers Jungersen, Esther Blanco, Jens Nielsen, Maria Montoya
Heterologous protection against swine influenza viruses (SwIVs) of different lineages is an important concern for the pig industry. Cross-protection between 'avian-like' H1N1 and 2009 pandemic H1N1 lineages has been observed previously, indicating the involvement of cross-reacting T-cells. Here, reverse vaccinology was applied to identify cross-reacting MHC class I T-cell epitopes from two different SwIV H1 lineages in pigs. In silico prediction followed by in vitro and in vivo testing was used to identify SLA-1*0702 T-cell epitopes in heterologous SwIV-infected pigs...
May 30, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28549876/prediction-and-analysis-of-promiscuous-t-cell-epitopes-derived-from-the-vaccine-candidate-antigens-of-leishmania-donovani-binding-to-mhc-class-ii-alleles-using-in-silico-approach
#7
Manju Kashyap, Varun Jaiswal, Umar Farooq
Visceral leishmaniasis is a dreadful infectious disease and caused by the intracellular protozoan parasites, Leishmania donovani and Leishmania infantum. Despite extensive efforts for developing effective prophylactic vaccine, still no vaccine is available against leishmaniasis. However, advancement in immunoinformatics methods generated new dimension in peptide based vaccine development. The present study was aimed to identify T-cell epitopes from the vaccine candidate antigens like Lipophosphogylcan-3(LPG-3) and Nucleoside hydrolase (NH) from the L...
May 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28549079/computational-modeling-of-immune-system-of-the-fish-for-a-more-effective-vaccination-in-aquaculture
#8
Alice Madonia, Cristiano Melchiorri, Simone Bonamano, Marco Marcelli, Chiara Bulfon, Filippo Castiglione, Marco Galeotti, Donatella Volpatti, Francesco Mosca, Pietro-Giorgio Tiscar, Nicla Romano
Motivation: A computational model equipped with the main immunological features of the sea bass ( Dicentrarchus labrax L. ) immune system was used to predict more effective vaccination in fish. The performance of the model was evaluated by using the results of two in vivo vaccinations trials against L. anguillarum and P. damselae . Tests were performed to select the appropriate doses of vaccine and infectious bacteria to set up the model. Simulation outputs were compared with the specific antibody production and the expression of BcR and TcR gene transcripts in spleen...
May 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28536262/in-silico-and-cell-based-analyses-reveal-strong-divergence-between-prediction-and-observation-of-t-cell-recognized-tumor-antigen-t-cell-epitopes
#9
Julien Schmidt, Philippe Guillaume, Danijel Dojcinovic, Julia Karbach, George Coukos, Immanuel Luescher
Tumor exomes provide comprehensive information on mutated, over-expressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T cell epitopes, because neoepitope specific T cells often are tumoricidal. However, identifying tumor-specific T cell epitopes is a major challenge. A widely used strategy relies on initial prediction of human leukocyte antigen binding peptides by in silico algorithms, but the predictive power of this approach is unclear...
May 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28534196/in-silico-analysis-of-shiga-toxins-stxs-to-identify-new-potential-vaccine-targets-for-shiga-toxin-producing-escherichia-coli
#10
Maryam Golshani, Mana Oloomi, Saeid Bouzari
Shiga toxins belong to a family of structurally and functionally related toxins serving as the main virulence factors for pathogenicity of the Shiga toxin-producing Escherichia coli (STEC) associating with Hemolytic uremic syndrome (HUS). At present, there is no effective treatment or prevention for HUS. The aim of the present study was to find conserved regions within the amino acid sequences of Stx1, Stx2 (Shiga toxin) and their variants. In this regard, In-silico identification of conformational continuous B cell and T-cell epitopes was performed in order to introduce new potential vaccine candidates...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28509875/in-silico-analysis-of-epitope-based-vaccine-candidates-against-hepatitis-b-virus-polymerase-protein
#11
Juzeng Zheng, Xianfan Lin, Xiuyan Wang, Liyu Zheng, Songsong Lan, Sisi Jin, Zhanfan Ou, Jinming Wu
Hepatitis B virus (HBV) infection has persisted as a major public health problem due to the lack of an effective treatment for those chronically infected. Therapeutic vaccination holds promise, and targeting HBV polymerase is pivotal for viral eradication. In this research, a computational approach was employed to predict suitable HBV polymerase targeting multi-peptides for vaccine candidate selection. We then performed in-depth computational analysis to evaluate the predicted epitopes' immunogenicity, conservation, population coverage, and toxicity...
May 16, 2017: Viruses
https://www.readbyqxmd.com/read/28496441/discovery-of-novel-leptospirosis-vaccine-candidates-using-reverse-and-structural-vaccinology
#12
André Alex Grassmann, Frederico Schmitt Kremer, Júlia Cougo Dos Santos, Jéssica Dias Souza, Luciano da Silva Pinto, Alan John Alexander McBride
Leptospira spp. are diderm (two membranes) bacteria that infect mammals causing leptospirosis, a public health problem with global implications. Thousands of people die every year due to leptospirosis, especially in developing countries with tropical climates. Prophylaxis is difficult due to multiple factors, including the large number of asymptomatic hosts that transmit the bacteria, poor sanitation, increasing numbers of slum dwellers, and the lack of an effective vaccine. Several leptospiral recombinant antigens were evaluated as a replacement for the inactivated (bacterin) vaccine; however, success has been limited...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28472201/predicting-hiv-1-transmission-and-antibody-neutralization-efficacy-in-vivo-from-stoichiometric-parameters
#13
Oliver F Brandenberg, Carsten Magnus, Peter Rusert, Huldrych F Günthard, Roland R Regoes, Alexandra Trkola
The potential of broadly neutralizing antibodies targeting the HIV-1 envelope trimer to prevent HIV-1 transmission has opened new avenues for therapies and vaccines. However, their implementation remains challenging and would profit from a deepened mechanistic understanding of HIV-antibody interactions and the mucosal transmission process. In this study we experimentally determined stoichiometric parameters of the HIV-1 trimer-antibody interaction, confirming that binding of one antibody is sufficient for trimer neutralization...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28471227/from-in-silico-immunogenicity-verification-to-in-vitro-expression-of-recombinant-core-ns3-fusion-protein-of-hcv
#14
S Hekmat, S D Siadat, M R Aghasadeghi, S M Sadat, G Bahramali, M M Aslani, M Mahdavi, S Shahbazi
BACKGROUND AND OBJECTIVE: Hepatitis C virus (HCV) is a serious global health burden. There is no effective vaccine against HCV and new direct acting antivirals (DAAs) are so expensive and virtually unavailable to the public. Therefore, seeking for therapeutic or prophylactic vaccines is exigent and reliever. METHODS: The secondary and tertiary structures of the recombinant Core-NS3 (rC-N) fusion protein of HCV and its B and T-cells epitopes were evaluated with bioinformatics software...
2017: Bratislavské Lekárske Listy
https://www.readbyqxmd.com/read/28466035/analysis-of-ebola-virus-polymerase-domains-to-find-strain-specific-differences-and-to-gain-insight-on-their-pathogenicity
#15
Seema Patel, Snigdha Patel
Ebola virus, a member of the family Filoviridae has caused immense morbidity and mortality in recent times, especially in West Africa. The infection characterized by chills, fever, diarrhea, and myalgia can progress to hemorrhage and death. Hence, it is a high priority area to better understand its biology in order to expedite vaccine development pipelines. In this regard, this study analyzes the domains in RNA polymerase of fifteen publicly-available Ebola isolates belonging to three strains (Zaire, Sudan and Reston)...
September 2016: Virusdisease
https://www.readbyqxmd.com/read/28435428/in-silico-cd4-cd8-t-cell-and-b-cell-immunity-associated-immunogenic-epitope-prediction-and-hla-distribution-analysis-of-zika-virus
#16
Essam Mohammed Janahi, Anupam Dhasmana, Vandana Srivastava, Aditya Narayan Sarangi, Sana Raza, Jamal M Arif, Madan Lal Bramha Bhatt, Mohtashim Lohani, Mohammed Yahya Areeshi, Anand Murari Saxena, Shafiul Haque
Zika virus (ZIKV) is a mosquito-borne flavivirus distributed all over Africa, South America and Asia. The infection with the virus may cause acute febrile sickness that clinically resembles dengue fever, yet there is no vaccine, no satisfactory treatment, and no means of evaluating the risk of the disease or prognosis in the infected people. In the present study, the efficacy of the host's immune response in reducing the risk of infectious diseases was taken into account to carry out immuno-informatics driven epitope screening strategy of vaccine candidates against ZIKV...
2017: EXCLI journal
https://www.readbyqxmd.com/read/28433326/status-of-the-development-of-a-vaccine-against-mycoplasma-bovis
#17
REVIEW
Jose Perez-Casal, Tracy Prysliak, Teresa Maina, Muhammad Suleman, Steve Jimbo
Mycoplasma bovis is an important pathogen of cattle and, despite numerous efforts an effective vaccine for control of the disease it causes remains elusive. Although we now know more about the biology of this pathogen, information is lacking about appropriate protective antigens, the type of immune response that confers protection and adjuvants selection. The use of conserved recombinant proteins, selected using in silico approaches, as components of a vaccine may be a better choice over bacterin-based vaccines due to the limited protection afforded by them and adverse reactions caused by them...
May 19, 2017: Vaccine
https://www.readbyqxmd.com/read/28411163/development-of-a-multi-epitope-peptide-vaccine-inducing-robust-t-cell-responses-against-brucellosis-using-immunoinformatics-based-approaches
#18
Mahdiye Saadi, Ahmad Karkhah, Hamid Reza Nouri
Current investigations have demonstrated that a multi-epitope peptide vaccine targeting multiple antigens could be considered as an ideal approach for prevention and treatment of brucellosis. According to the latest findings, the most effective immunogenic antigens of brucella to induce immune responses are included Omp31, BP26, BLS, DnaK and L7-L12. Therefore, in the present study, an in silico approach was used to design a novel multi-epitope vaccine to elicit a desirable immune response against brucellosis...
April 11, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28392143/development-of-a-dna-vaccine-expressing-a-secreted-hiv-1-gp41-ectodomain-that-includes-the-membrane-proximal-external-region
#19
Luca Melnychuk, Lara Ajamian, Patrick Jean-Pierre, Jiaming Liang, Romina Gheorghe, Mark A Wainberg, Gerasimos J Zaharatos
A limited number of sites on the HIV-1 Envelope protein are vulnerable to broadly neutralizing antibodies (bnAbs). One of these sites, the membrane proximal external region (MPER), is located at the C-terminus of the gp41 ectodomain (gp41ecto). This highly conserved sequence is bound by several well-characterized bnAbs. Efforts to produce a gp41 immunogen are in part hampered by the MPER's hydrophobicity and propensity to induce aggregation. We sought to produce a DNA vaccine expressing a gp41ecto that is both secreted from mammalian cells and maintains binding by bnAbs to the MPER...
May 9, 2017: Vaccine
https://www.readbyqxmd.com/read/28389892/in-silico-identification-and-validation-of-a-novel-hypothetical-protein-in-cryptosporidium-hominis-and-virtual-screening-of-inhibitors-as-therapeutics
#20
Arpit Kumar Shrivastava, Subrat Kumar, Priyadarshi Soumyaranjan Sahu, Rajani Kanta Mahapatra
Computational approaches to predict structure/function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are ineffective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines...
April 7, 2017: Parasitology Research
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