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In silico vaccine

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https://www.readbyqxmd.com/read/29143375/an-immunoinformatics-approach-to-define-t-cell-epitopes-from-polyketide-and-non-ribosomal-peptide-synthesis-proteins-of-mycobacterium-tuberculosis-as-potential-vaccine-candidates
#1
S Dhivya, V Baskar, S R Kumar, R Sathishkumar
The role of polyketide and non-ribosomal proteins from the class of small molecule metabolism of Mycobacterium tuberculosis is well documented in envelope organization, virulence, and pathogenesis. Consequently, the identification of T cell epitopes from these proteins could serve to define potential antigens for the development of vaccines. Fourty-one proteins from polyketide and non-ribosomal peptide synthesis of small molecule metabolism proteins of M tuberculosis H37Rv were analyzed computationally for the presence of HLA class I binding nanomeric peptides...
November 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29140228/co-factor-independent-phosphoglycerate-mutase-of-leishmania-donovani-modulates-macrophage-signalling-and-promotes-t-cell-repertoires-bearing-epitopes-for-both-mhc-i-and-mhc-ii
#2
Manish K Singh, Fauzia Jamal, Amit K Dubey, Pushkar Shivam, Sarita Kumari, Pushpanjali, Ghufran Ahmed, Manas R Dikhit, S Narayan, V N R DAS, Krishna Pandey, K K Sinha, P DAS, Shubhankar K Singh
Immunoactivation depends upon the antigen potential to modulate T-cell repertoires. The present study has enumerated the effect of 61 kDa recombinant Leishmania donovani co-factor-independent phosphoglycerate mutase (rLd-iPGAM) on mononuclear cells of healthy and treated visceral leishmaniasis subjects as well as on THP-1 cell line. rLd-iPGAM stimulation induced higher expression of interleukin-1β (IL-1β) in the phagocytic cell, its receptor and CD69 on T-cell subsets. These cellular activations resulted in upregulation of host-protective cytokines IL-2, IL-12, IL-17, tumour necrosis factor-α and interferon-γ, and downregulation of IL-4, IL-10 and tumour growth factor-β...
November 15, 2017: Parasitology
https://www.readbyqxmd.com/read/29138085/in-silico-design-cloning-expression-and-immunologic-evaluation-of-ed-fusion-protein-of-nt-h-influenzae
#3
Ava Behrouzi, Saeid Bouzari, Mana Oloomi, Abolfaz Fateh, Farzam Vaziri, Parviz Afrough, Amir Amanzadeh, Seyed Davar Siadat
Infections due to nontypeable Haemophilus influenzae (NTHi) are important causes of child mortality throughout the world. Given the lack of effective vaccines for these strains and the spread and prevalence of these infections in the world, it is necessary to design novel vaccine candidates against these strains. D and E proteins are conserved membrane-specific lipoproteins among encapsulated and non-encapsulated H. influenza strains, which, according to the exposure surface and conservation degree between both strains, can be considered as vaccine candidates suitable for studies...
November 11, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29133159/highly-conserved-exposed-immunogenic-peptides-of-omp34-against-acinetobacter-baumannii-an-innovative-approach
#4
Abolfazl Jahangiri, Iraj Rasooli, Parviz Owlia, Abbas Ali Imani Fooladi, Jafar Salimian
Omp34, also known as Omp34kDa or Omp33-36 is a virulence factor associated with A. baumannii metabolic fitness or its adherence and invasion to human epithelial cells. This protein is also introduced as a specific antigen which could induce strong antibody responses. In the present in silico study, recent vaccine design strategies such as 'antigen minimization' and 'high epitope density' were invoked to design a soluble immunogen with higher antigenicity. As an advantage, the tools employed in the current study are easily available...
November 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29128519/genetic-structure-of-two-erythrocyte-binding-antigens-of-plasmodium-falciparum-reveals-a-contrasting-pattern-of-selection
#5
Pramita Chowdhury, Srikanta Sen, Sumana Datta Kanjilal, Sanghamitra Sengupta
Erythrocyte binding antigens 175 (EBA-175) and 140 (EBA-140) play key roles in erythrocyte invasion by binding to glycophorin A (GPA) and C (GPC) respectively in human malaria. Since antigenic variation in malaria endemic region is a major barrier to development of effective vaccine, we explore the nature and pattern of sequence diversity of these two vaccine candidates in Kolkata, India. Population genetic parameters based on parasite sequences representing region II of Pfeba-175 and Pfeba-140 genes were estimated using DnaSP V...
November 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29121936/molecular-characterization-of-a-novel-muscovy-duck-parvovirus-isolate-evidence-of-recombination-between-classical-mdpv-and-goose-parvovirus-strains
#6
Jianye Wang, Jueyi Ling, Zhixian Wang, Yu Huang, Jianzhong Zhu, Guoqiang Zhu
BACKGROUND: Muscovy duck parvovirus (MDPV) and Goose parvovirus (GPV) are important etiological agents for Muscovy duck parvoviral disease and Derzsy's disease, respectively; both of which can cause substantial economic losses in waterfowl industry. In contrast to GPV, the complete genomic sequence data of MDPV isolates are still limited and their phylogenetic relationships largely remain unknown. In this study, the entire genome of a pathogenic MDPV strain ZW, which was isolated from a deceased Muscovy duckling in 2006 in China, was cloned, sequenced, and compared with that of other classical MDPV and GPV strains...
November 9, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29114400/an-untypeable-enterotoxigenic-escherichia-coli-represents-one-of-the-dominant-types-causing-human-disease
#7
Atsushi Iguchi, Astrid von Mentzer, Taisei Kikuchi, Nicholas R Thomson
Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhoea in children below 5 years of age in endemic areas, and is a primary cause of diarrhoea in travellers visiting developing countries. Epidemiological analysis of E. coli pathovars is traditionally carried out based on the results of serotyping. However, genomic analysis of a global ETEC collection of 362 isolates taken from patients revealed nine novel O-antigen biosynthesis gene clusters that were previously unrecognized, and have collectively been called unclassified...
September 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29100164/in-silico-design-of-knowledge-based-plasmodium-falciparum-epitope-ensemble-vaccines
#8
Shymaa Abdullah Damfo, Pedro Reche, Derek Gatherer, Darren R Flower
Malaria is a global health burden, and a major cause of mortality and morbidity in Africa. Here we designed a putative malaria epitope ensemble vaccine by selecting an optimal set of pathogen epitopes. From the IEDB database, 584 experimentally-verified CD8+ epitopes and 483 experimentally-verified CD4+ epitopes were collected; 89% of which were found in 8 proteins. Using the PVS server, highly conserved epitopes were identified from variability analysis of multiple alignments of Plasmodium falciparum protein sequences...
October 12, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29091543/in-silico-design-of-a-novel-chimeric-shigella-ipab-fused-to-c-terminal-of-clostridium-perfringens-enterotoxin-as-a-vaccine-candidate
#9
Sina Arabshahi, Bahar Nayeri Fasaei, Abdollah Derakhshandeh, Aytak Novinrooz
This study aimed to design a novel chimeric protein in silico to serve as a serotype-independent vaccine candidate against Shigella. The chimera contains amino acid residues 240-460 of Shigella invasion plasmid antigen B (IpaB) and the C-terminus of Clostridium perfringens enterotoxin (C-CPE). Amino acid sequences of 537 peptide linkers were obtained from two protein linker databases. 3D structures of IpaB-CPE290-319, IpaB-CPE184-319, IpaB-CPE194-319 and 537 newly designed IpaB-linker-CPE290-319 constructs with varying linker regions were predicted...
November 1, 2017: Bioengineered
https://www.readbyqxmd.com/read/29090192/identification-of-new-virulence-factors-and-vaccine-candidates-for-yersinia-pestis
#10
Jourdan A Andersson, Jian Sha, Tatiana E Erova, Eric C Fitts, Duraisamy Ponnusamy, Elena V Kozlova, Michelle L Kirtley, Ashok K Chopra
Earlier, we reported the identification of new virulence factors/mechanisms of Yersinia pestis using an in vivo signature-tagged mutagenesis (STM) screening approach. From this screen, the role of rbsA, which encodes an ATP-binding protein of ribose transport system, and vasK, an essential component of the type VI secretion system (T6SS), were evaluated in mouse models of plague and confirmed to be important during Y. pestis infection. However, many of the identified genes from the screen remained uncharacterized...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29062895/norovirus-escape-from-broadly-neutralizing-antibodies-is-limited-to-allostery-like-mechanisms
#11
Abimbola O Kolawole, Hong Q Smith, Sophia A Svoboda, Madeline S Lewis, Michael B Sherman, Gillian C Lynch, B Montgomery Pettitt, Thomas J Smith, Christiane E Wobus
Ideal antiviral vaccines elicit antibodies (Abs) with broad strain recognition that bind to regions that are difficult to mutate for escape. Using 10 murine norovirus (MNV) strains and 5 human norovirus (HuNoV) virus-like particles (VLPs), we identified monoclonal antibody (MAb) 2D3, which broadly neutralized all MNV strains tested. Importantly, escape mutants corresponding to this antibody were very slow to develop and were distal to those raised against our previously studied antibody, A6.2. To understand the atomic details of 2D3 neutralization, we determined the cryo-electron microscopy (cryo-EM) structure of the 2D3/MNV1 complex...
September 2017: MSphere
https://www.readbyqxmd.com/read/29056423/effect-of-recombinant-glutathione-s-transferase-as-vaccine-antigen-against-rhipicephalus-appendiculatus-and-rhipicephalus-sanguineus-infestation
#12
Gabriela Alves Sabadin, Luís Fernando Parizi, Irene Kiio, Marina Amaral Xavier, Renata da Silva Matos, Maria Izabel Camargo-Mathias, Naftaly Wang'ombe Githaka, Vish Nene, Itabajara da Silva Vaz
The ticks Rhipicephalus appendiculatus and Rhipicephalus sanguineus are the main vectors of Theileria parva and Babesia spp. in cattle and dogs, respectively. Due to their impact in veterinary care and industry, improved methods against R. appendiculatus and R. sanguineus parasitism are under development, including vaccines. We have previously demonstrated the induction of a cross-protective humoral response against Rhipicephalus microplus following vaccination with recombinant glutathione S-transferase from Haemaphysalis longicornis tick (rGST-Hl), suggesting that this protein could control tick infestations...
October 19, 2017: Vaccine
https://www.readbyqxmd.com/read/29049350/an-integrative-in-silico-approach-for-therapeutic-target-identification-in-the-human-pathogen-corynebacterium-diphtheriae
#13
Syed Babar Jamal, Syed Shah Hassan, Sandeep Tiwari, Marcus V Viana, Leandro de Jesus Benevides, Asad Ullah, Adrián G Turjanski, Debmalya Barh, Preetam Ghosh, Daniela Arruda Costa, Artur Silva, Richard Röttger, Jan Baumbach, Vasco A C Azevedo
Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms...
2017: PloS One
https://www.readbyqxmd.com/read/29032900/in-silico-vaccine-strain-prediction-for-human-influenza-viruses
#14
REVIEW
Thorsten R Klingen, Susanne Reimering, Carlos A Guzmán, Alice C McHardy
Vaccines preventing seasonal influenza infections save many lives every year; however, due to rapid viral evolution, they have to be updated frequently to remain effective. To identify appropriate vaccine strains, the World Health Organization (WHO) operates a global program that continually generates and interprets surveillance data. Over the past decade, sophisticated computational techniques, drawing from multiple theoretical disciplines, have been developed that predict viral lineages rising to predominance, assess their suitability as vaccine strains, link genetic to antigenic alterations, as well as integrate and visualize genetic, epidemiological, structural, and antigenic data...
October 9, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/29032659/in-silico-analysis-of-putative-drug-and-vaccine-target-of-the-metabolic-pathways-of-actinobacillus-pleuropneumoniae-using-subtractive-comparative-genomics-approach
#15
Biruk Tesfaye Birhanu, Seung-Jin Lee, Na-Hye Park, Ju-Beom Song, Seung-Chun Park
Actinobacillus pleuropneumoniae is a gram-negative bacterium residing in the respiratory tract of pigs that causes porcine respiratory disease complex, which leads to significant losses in the pig industry worldwide. The incidence of drug resistance in this bacterium is increasing; thus, identifying new protein/gene targets for drug and vaccine development is critical. In this study, we used an in silico approach, utilizing several databases, including Kyoto Encyclopedia of Genes and Genomes (KEGG), the database of essential genes (DEG), DrugBank, and Swiss-Prot, to identify non-homologous essential genes and prioritize these proteins for their druggability...
October 13, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/28984500/ursolic-acid-and-carvacrol-may-be-potential-inhibitors-of-dormancy-protein-small-heat-shock-protein16-3-of-mycobacterium-tuberculosis
#16
Babban Jee, Sanjay Kumar, Renu Yadav, Yogesh Singh, Anuj Kumar, Naveen Sharma
Small heat shock protein16.3 (sHSP16.3) is a crucial protein for survival of Mycobacterium tuberculosis (MTB) in its host. Besides, this protein acts as a molecular chaperone during stress and is indispensable for MTB's growth, virulence and cell wall thickening. sHSP16.3 is also a promising candidate for vaccine, serodiagnosis and drug design as well. In the present study, we have targeted sHSP16.3 with two phytochemicals namely ursolic acid and carvacrol using in silico approach. Molecular docking analysis showed that both phytochemicals (ursolic acid and carvacrol) has docked with sHSP16...
October 6, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28981210/proteome-and-structural-organization-of-the-knob-complex-on-the-surface-of-the-plasmodium-infected-red-blood-cell
#17
ShubaVarshini Alampalli, Manish Grover, Syama Chandran, Utpal Tatu, Pragyan Achary
PURPOSE: The cell membrane of the erythrocytes infected with the malaria parasite Plasmodium falciparum undergoes several changes during the course of parasite life cycle and forms protrusions known as 'knobs' on its surface during the mature trophozoite and schizont stages. The structural organization of knob components especially PfEMP1 on the iRBC surface is the main determinant for the cytoadhesive and rosetting capacity of the iRBC by binding to various host receptors as well as for the variable antigenicity, which is crucial for immunoevasion...
October 5, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28976983/protection-of-bats-eptesicus-fuscus-against-rabies-following-topical-or-oronasal-exposure-to-a-recombinant-raccoon-poxvirus-vaccine
#18
Ben Stading, James A Ellison, William C Carson, Panayampalli Subbian Satheshkumar, Tonie E Rocke, Jorge E Osorio
Rabies is an ancient neglected tropical disease that causes tens of thousands of human deaths and millions of cattle deaths annually. In order to develop a new vaccine for potential use in bats, a reservoir of rabies infection for humans and animals alike, an in silico antigen designer tool was used to create a mosaic glycoprotein (MoG) gene using available sequences from the rabies Phylogroup I glycoprotein. This sequence, which represents strains more likely to occur in bats, was cloned into raccoonpox virus (RCN) and the efficacy of this novel RCN-MoG vaccine was compared to RCN-G that expresses the glycoprotein gene from CVS-11 rabies or luciferase (RCN-luc, negative control) in mice and big brown bats (Eptesicus fuscus)...
October 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28976134/tumor-protein-53-mutations-mapping-to-its-tertiary-structure-with-in-silico-prediction-of-neoepitopic-vaccine-candidates-in-bone-tumors
#19
Hamid Nawaz Tipu, Abdul Rehman Arshad
Mapping of tp 53 mutations in bone cancers present in COSMIC database to its secondary and tertiary structure with in silico prediction of newly formed HLA binding epitopes as candidates for synthetic peptide vaccine. Mutations in bone cancers present in COSMIC database were listed and manually induced in wt p53 FASTA sequence. Wt p53 secondary structure was predicted. Template identified and tertiary structure of wt p53 was modelled in Cn3D followed by individual mutations mapping onto this model. HLA class I binding affinity was determined for mutated sequences to determine any newly binding peptide sequences...
September 2017: Journal of Experimental Therapeutics & Oncology
https://www.readbyqxmd.com/read/28974324/in-silico-analysis-and-in-vitro-evaluation-of-immunogenic-and-immunomodulatory-properties-of-promiscuous-peptides-derived-from-leishmania-infantum-eukaryotic-initiation-factor
#20
Olga S Koutsoni, John G Routsias, Ioannis D Kyriazis, Mourad Barhoumi, Ikram Guizani, Athanassios Tsakris, Eleni Dotsika
It is generally considered as imperative the ability to control leishmaniasis through the development of a protective vaccine capable of inducing long-lasting and protective cell-mediated immune responses. In this current study, we demonstrated potential epitopes that bind to H2 MHC class I and II molecules by conducting the in silico analysis of Leishmania infantum eukaryotic Initiation Factor (LieIF) protein, using online available algorithms. Moreover, we synthesized five peptides (16-18 amino acids long) which are part of the N-terminal portion of LieIF and contain promising MHC class I and II-restricted epitopes and afterwards, their predicted immunogenicity was evaluated in vitro by monitoring peptide-specific T-cell responses...
November 1, 2017: Bioorganic & Medicinal Chemistry
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