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In silico vaccine

Liam V Brown, Eamonn A Gaffney, Jonathan Wagg, Mark C Coles
Tumour immunotherapy is dependent upon activation and expansion of tumour-targetting immune cells, known as cytotoxic T-lymphocytes (CTLs). Cancer vaccines developed in the past have had limited success and the mechanisms resulting in failure are not well characterized. To elucidate these mechanisms, we developed a human-parametrized, in silico , agent-based model of vaccination-driven CTL activation within a clinical short-peptide vaccination context. The simulations predict a sharp transition in the probability of CTL activation, which occurs with variation in the separation rate (or off-rate) of tumour-specific immune response-inducing peptides (cognate antigen) from the major histocompatibility class I (MHC-I) receptors of dendritic cells (DCs) originally at the vaccination site...
March 2018: Journal of the Royal Society, Interface
Aruna Narula, Rajan Kumar Pandey, Nazia Khatoon, Amit Mishra, Vijay Kumar Prajapati
Chikungunya infection has been a cause of countless deaths worldwide. Due to lack of permanent treatment and prevention of this disease, the mortality rate remains very high. Therefore, we followed an immunoinformatics approach for the development of multi-epitope subunit vaccine which is able to elucidate humoral, cell-mediated and innate immune responses inside the host body. Both structural and non-structural proteins of chikungunya virus were utilized for prediction of B-cell and T-cell binding epitopes along with interferon-γ (IFN-γ) inducing epitopes...
March 10, 2018: Infection, Genetics and Evolution
Maryam Golshani, Melina Ghasemian, Nematollah Gheibi, Saeid Bouzari
Background: L7/L12 is a protective antigen conserved in main Brucella pathogens and is considered as potential vaccine candidate. Outer membrane protein 2b is an immunogen conserved in all Brucella pathogens. Materials and Methods: The purpose of the current study was to in silico design a L7/L12-SOmp2b fusion protein and in vitro production of the chimera. Two possible fusion forms, L7/L12-SOmp2b and SOmp2b-L7/L12, were subjected to in silico modeling and analysis...
2018: Advanced Biomedical Research
Alireza Salimi Chirani, Robabeh Majidzadeh, Ramin Pouriran, Mohsen Heidary, Mohammad Javad Nasiri, Mehrdad Gholami, Mehdi Goudarzi, Vahid Fallah Omrani
The vaccine candidates that have been introduced for immunization against Pseudomonas aeruginosa (P. aeruginosa) strains are quite diverse. In fact, there has been no proper antigen to act as an effective immunogenic substance against this ubiquitous pathogen in the market as yet. The complications caused by this bacterium due to the rapid development of multiple drug resistant strains have led to clinical problems worldwide. P. aeruginosa encodes many specific virulence elements that could be used as appropriate vaccine candidates...
February 5, 2018: Computational Biology and Chemistry
Sajad Abdollahi, Iraj Rasooli, Seyed Latif Mousavi Gargari
Acinetobacter baumannii is an opportunistic multidrug resistant pathogen. TonB-dependent copper receptor is an outer membrane protein and has a role in binding of A. baumannii to host cell via attachment to fibronectin. Moreover, it is highly expressed in biofilm community. In this study the properties of copper receptor were analyzed in silico and its vaccine potential was investigated. TonB-dependent copper and iron receptor domains plus one plug domain at N-terminal were determined by domain analysis. Topology modeling showed 22 β-strands, 11 loops and 10 periplasmic turns...
March 7, 2018: Microbial Pathogenesis
Faidad Khan, Mohsin Ahmad Khan, Nadeem Ahmed, Muhammad Islam Khan, Hamid Bashir, Saad Tahir, Ahmad Usman Zafar
INTRODUCTION: Pakistan has one of the highest burdens of pneumococcal diseases in the world, but unfortunately studies in this demanding research area are limited in the region. Pneumococcal surface protein A (PspA) is the next generation pneumococcal vaccine candidate as the protein locates on the Streptococcus pneumoniae surface. Its gene, pspA, might be encoded by all pneumococci, and the protein has proven immunogenicity. The molecular characterization of PspA, pneumococcal serotype distribution and antibiotic susceptibility are important for regional diversity studies...
March 9, 2018: Infectious Diseases and Therapy
Varun Chauhan, Mini P Singh, Radha K Ratho
Hepatitis C virus (HCV) infects almost 150 million people and is a leading cause of liver disease worldwide. It has been classified into seven genotypes; the most common genotype affecting Indian population is genotype 3 (60-70%). Currently there is no vaccine for any genotype of HCV. In order to develop peptide based vaccine against HCV, it is important to identify the conservancy in the circulating genotypes, along with the Human Leucocyte Antigen (HLA) alleles in the target population. The present study aims to identify conserved CD4 and CD8 T cells and B cell epitopes against Indian HCV-genotype-3a using an in silico analysis...
March 5, 2018: Biologicals: Journal of the International Association of Biological Standardization
Subramaniyan Vijayakumar, Venkatachalam Ramesh, Srinivasan Prabhu, Palani Manogar
Reverse vaccinology method was used to predict the monovalent peptide vaccine candidate to produce antibodies for therapeutic purpose and to predict tetravalent vaccine candidate to act as a common vaccine to cover all the fever dengue virus serotypes. Envelope (E)-proteins of DENV-1-4 serotypes were used for vaccine prediction using NCBI, Uniprot/Swissprot, Swiss-prot viewer, VaxiJen V2.0, TMHMM, BCPREDS, Propred-1, Propred and MHC Pred,. E-proteins of DENV-1-4 serotypes were identified as antigen from which T cell epitopes, through B cell epitopes, were predicted to act as peptide vaccine candidates...
November 1, 2017: Journal of Biomedical Research
Dickson Kinyanyi, George Obiero, George F O Obiero, Peris Amwayi, Stephen Mwaniki, Mark Wamalwa
African swine fever virus (ASFV) is the etiological agent of ASF, a fatal hemorrhagic fever that affects domestic pigs. There is currently no vaccine against ASFV, making it a significant threat to the pork industry. The ASFV genome sequence has been published; however, about half of ASFV open reading frames have not been characterized in terms of their structure and function despite being essential for our understanding of ASFV pathogenicity. The present study reports the three-dimensional structure and function of uncharacterized protein, pB263R (NP_042780...
2018: PeerJ
Syed S Hassan, Syed B Jamal, Leandro G Radusky, Sandeep Tiwari, Asad Ullah, Javed Ali, Behramand, Paulo V S D de Carvalho, Rida Shams, Sabir Khan, Henrique C P Figueiredo, Debmalya Barh, Preetam Ghosh, Artur Silva, Jan Baumbach, Richard Röttger, Adrián G Turjanski, Vasco A C Azevedo
Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the "pocketome druggability." To this end, we first computed the "modelome" (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (∼9%) structure models...
2018: Frontiers in Genetics
Pramod Kumar Maurya, Swati Singh, Ashutosh Mani
Antibiotic resistance is increasing rapidly in pathogenic organisms, creating more complications for treatment of diseases. Rocky Mountain spotted fever (RMSF) is a neglected tropical disease in humans caused by Rickettsia rickettsii for which no effective therapeutic is available. Subtractive genomics methods facilitate the characterization of non-homologous essential proteins that could be targeted for the discovery of potential therapeutic compounds against R. rickettsii to combat RMSF. Present study followed an in-silico based methodology, involving scanning and filtering the complete proteome of Rickettsia rickettsii by using several prioritization parameters in the search of potential candidates for drug development...
February 20, 2018: Acta Tropica
Fengbo Wu, Yan Huang, Peng Zhang, Chunting Wang, Yaomei Tian, Lian Lu, Gu He, Li Yang
This study presents a rational design approach to discovery synthetic peptide vaccine candidates from endogenous proteins for chronic non-infectious diseases immunological therapeutics. The approach described the screening of key antigenic amino acid residues of the interleukine-13, which is up-regulated expression in asthma, followed by the development of immunological helper epitope peptides via an integrative computational and experimental method. Notably, this totally synthetic peptide vaccine was capable of stimulating humoral immune responses much stronger than those of parental antigenic peptides by enhancing the efficiency of antigen presentation, and had effective treatment in mouse asthma models...
January 23, 2018: Oncotarget
Gayeon Won, John Hwa Lee
The obligate intracellular Lawsonia intracellularis (LI), the etiological agent of proliferative enteropathy (PE), is an economically important disease in the swine industry. Due to extreme difficulty of in vitro culture of the pathogen, molecular characterization of protein components of LI that are targets of the immune system, is difficult; thus, the scientific evidence to drive the development of preventive measures is lacking. In this work, we investigated the antigenic and functional characteristics of a putative flagellar-associated protein, LI0570, using in silico computational approaches for epitope prediction and an in vitro protein-based molecular assay...
February 15, 2018: Veterinary Research
Emma Christine Jappe, Jens Kringelum, Thomas Trolle, Morten Nielsen
Peptides that bind to and are presented by MHC class I and class II molecules collectively make up the immunopeptidome. In the context of vaccine development, an understanding of the immunopeptidome is essential, and much effort has been dedicated to its accurate and cost-effective identification. Current state-of-the-art methods mainly comprise in silico tools for predicting MHC binding which is strongly correlated with peptide immunogenicity. However, only a small proportion of the peptides that bind to MHC molecules are, in fact, immunogenic, and substantial work has been dedicated to uncovering additional determinants of peptide immunogenicity...
February 15, 2018: Immunology
Vida Eraghi, Abdollah Derakhshandeh, Arsalan Hosseini, Azar Motamedi-Boroojeni
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne's disease in ruminants and there has been a shift in the public health approach to MAP and human diseases like Crohn's disease. The prevention of infection by MAP in ruminants is thought to deter the high impact of economic losses in the level of dairy industry and possible spreading of this pathogen in dairy products. The present study was done to investigate the construction and expression of the soluble form of a novel fusion protein, consisting of Heparin-binding hemagglutinin (HBHA) and high antigenic region of Fibronectin Attachment Protein-P (FAP-P), in order to introduce as a Th1 inducer subunit vaccine against MAP...
December 2017: Molecular Biology Research Communications
Philippe A Robert, Andrea Lj Marschall, Michael Meyer-Hermann
Vaccines against mutating pathogens such as influenza, HIV, or plasmodium are poorly protective towards new evolving strains. Rare individuals naturally mount broadly neutralizing antibodies covering most strains, but the requirements for their induction are unknown. The antibody response to vaccination has been recapitulated by in silico models that proposed two opposite schemes: A theory of 'frustration' where one epitope at a time leads to optimal antibody breadth through sequential immunizations, that was proven successful for HIV vaccination in primates...
February 1, 2018: Current Opinion in Biotechnology
Yelda Asad, Sajjad Ahmad, Thanyada Rungrotmongkol, Kara E Ranaghan, Syed Sikander Azam
The bacterium Providencia stuartii, is associated with urinary tract infections and is the most common cause of purple urine bag syndrome. The increasing multi-drug resistance pattern shown by the pathogen and lack of licensed vaccines make treatment of infections caused by P. stuartii challenging. As vaccinology data against the pathogen is scarce, an in silico proteome based Reverse Vaccinology (RV) protocol, in combination with subtractive proteomics is introduced in this work to screen potential vaccine candidates against P...
January 31, 2018: Journal of Molecular Graphics & Modelling
Wei-Lian Tan, Yean Kee Lee, Yen Fong Ho, Rohana Yusof, Noorsaadah Abdul Rahman, Saiful Anuar Karsani
Dengue is endemic throughout tropical and subtropical regions of the world. Currently, there is no clinically approved therapeutic drug available for this acute viral infection. Although the first dengue vaccine Dengvaxia has been approved for use in certain countries, it is limited to those without a previous dengue infection while the safety and efficacy of the vaccine in those elderly and younger children still need to be identified. Therefore, it is becoming increasingly important to develop therapeutics/drugs to combat dengue virus (DENV) infection...
2018: PeerJ
Hendrik Luxenburger, Franziska Graß, Janina Baermann, Tobias Boettler, Matthias Marget, Florian Emmerich, Marcus Panning, Robert Thimme, Katja Nitschke, Christoph Neumann-Haefelin
Virus-specific CD8+ T-cell responses play an important role in the outcome of hepatitis C virus (HCV) infection. To date, most HCV-specific CD8+ T-cell epitopes have been defined in HCV genotype 1 infection. In contrast, the HCV genotype 4-specific CD8+ T-cell response is poorly defined. Here, we analyzed whether known HCV-specific CD8+ T-cell epitopes are also recognized in HCV genotype 4-infected patients and set out to identify the first HCV genotype 4-specific CD8+ T-cell epitopes. We studied patients chronically infected with HCV genotype 1 (n=20) or 4 (n=21) using 91 well-described HCV-specific epitope peptides...
February 3, 2018: Journal of Viral Hepatitis
Rajan Kumar Pandey, Vijay Kumar Prajapati
Visceral leishmaniasis (VL) is caused by the parasites of Leishmania donovani complex, leads to the death of 20,000-40,000 people from 56 affected countries, worldwide. Till date, there is not a single available vaccine candidate to prevent the visceral leishmaniasis infection, and treatment only relies upon expensive and toxic chemotherapeutic options. Consequently, immunoinformatics approach was applied to design a multi-epitope based subunit vaccine to enhance the humoral as well as cell mediated immunity...
January 29, 2018: Journal of Cellular Biochemistry
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