keyword
MENU ▼
Read by QxMD icon Read
search

In silico vaccine

keyword
https://www.readbyqxmd.com/read/27928487/immunoreactivity-evaluation-of-a-new-recombinant-chimeric-protein-against-brucella-in-the-murine-model
#1
Abbas Abdollahi, Shahla Mansouri, Jafar Amani, Mahdi Fasihi-Ramandi, Mohammad Moradi
BACKGROUND AND OBJECTIVES: Brucellosis is an important health problem in developing countries and no vaccine is available for the prevention of infection in humans. Because of clinically infectious diseases and their economic consequences in human and animals, designing a proper vaccine against Brucella is desirable. In this study, we evaluated the immune responses induced by a designed recombinant chimera protein in murine model. MATERIALS AND METHODS: Three immunodominant antigens of Brucella have been characterized as potential immunogenic and protective antigens including: trigger factor (TF), Omp31 and Bp26 were fused together by EAAAK linkers to produce a chimera (structure were designed in silico), which was synthesized, cloned, and expressed in E...
June 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/27875780/vp1-residues-around-the-five-fold-axis-of-enterovirus-a71-mediate-heparan-sulfate-interaction
#2
Chee Wah Tan, I-Ching Sam, Vannajan Sanghiran Lee, Hui Vern Wong, Yoke Fun Chan
Enterovirus A71 (EV-A71) is a neurotropic enterovirus that uses heparan sulfate as an attachment receptor. The molecular determinants of EV-A71-heparan sulfate interaction are unknown. With In silico heparin docking and mutagenesis of all possible lysine residues in VP1, we identified that K162, K242 and K244 are responsible for heparin interaction and inhibition. EV-A71 mutants with K242A and K244A rapidly acquired compensatory mutations, T100K or E98A, and Q145R-T237N respectively, which restored the heparin-binding phenotype...
November 19, 2016: Virology
https://www.readbyqxmd.com/read/27872794/in-silico-identification-of-potential-peptides-or-allergen-shot-candidates-against-aspergillus-fumigatus
#3
Raman Thakur, Jata Shankar
Aspergillus fumigatus is capable of causing invasive aspergillosis or acute bronchopulmonary aspergillosis, and the current situation is alarming. There are no vaccine or allergen shots available for Aspergillus-induced allergies. Thus, a novel approach in designing of an effective vaccine or allergen shot candidate against A. fumigatus is needed. Using immunoinformatics approaches from the characterized A. fumigatus allergens, we have mapped epitopic regions to predict potential peptides that elicit both Aspergillus-specific T cells and B cell immune response...
2016: BioResearch Open Access
https://www.readbyqxmd.com/read/27834872/unraveling-the-roots-of-selectivity-of-peptide-affinity-reagents-for-structurally-similar-ribosomal-inactivating-protein-derivatives
#4
Deborah A Sarkes, Margaret M Hurley, Dimitra N Stratis-Cullum
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms...
November 9, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27828989/predicted-enhanced-human-propensity-of-current-avian-like-h1n1-swine-influenza-virus-from-china
#5
Veljko Veljkovic, Nevena Veljkovic, Slobodan Paessler, Marco Goeijenbier, Vladimir Perovic, Sanja Glisic, Claude P Muller
Influenza A virus (IAV) subtypes against which little or no pre-existing immunity exists in humans represent a serious threat to global public health. Monitoring of IAV in animal hosts is essential for early and rapid detection of potential pandemic IAV strains to prevent their spread. Recently, the increased pandemic potential of the avian-like swine H1N1 IAV A/swine/Guangdong/104/2013 has been suggested. The virus is infectious in humans and the general population seems to lack neutralizing antibodies against this virus...
2016: PloS One
https://www.readbyqxmd.com/read/27816827/in-silico-designing-breast-cancer-peptide-vaccine-for-binding-to-mhc-class-i-and-ii-a-molecular-docking-study
#6
Manijeh Mahdavi, Violaine Moreau
Antigenic peptides or cancer peptide vaccines can be directly delivered to cancer patients to produce immunologic responses against cancer cells. Specifically, designed peptides can associate with Major Histocompatibility Complex (MHC) class I or II molecules on the cell surface of antigen presenting cells activating anti-tumor effector mechanisms by triggering helper T cell (Th) or cytotoxic T cells (CTL). In general, high binding to MHCs approximately correlates with in vivo immunogenicity. Consequently, a molecular docking technique was run on a library of novel discontinuous peptides predicted by PEPOP from Human epidermal growth factor receptor 2 (HER2 ECD) subdomain III...
October 19, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27812412/in-silico-study-on-anti-chikungunya-virus-activity-of-hesperetin
#7
Adrian Oo, Pouya Hassandarvish, Sek Peng Chin, Vannajan Sanghiran Lee, Sazaly Abu Bakar, Keivan Zandi
BACKGROUND: The re-emerging, Aedes spp. transmitted Chikungunya virus (CHIKV) has recently caused large outbreaks in a wide geographical distribution of the world including countries in Europe and America. Though fatalities associated with this self-remitting disease were rarely reported, quality of patients' lives have been severely diminished by polyarthralgia recurrence. Neither effective antiviral treatment nor vaccines are available for CHIKV. Our previous in vitro screening showed that hesperetin, a bioflavonoid exhibits inhibitory effect on the virus intracellular replication...
2016: PeerJ
https://www.readbyqxmd.com/read/27806091/immunodominant-igm-and-igg-epitopes-recognized-by-antibodies-induced-in-enterovirus-a71-associated-hand-foot-and-mouth-disease-patients
#8
Kam Leng Aw-Yong, I-Ching Sam, Mia Tuang Koh, Yoke Fun Chan
Enterovirus A71 (EV-A71) is one of the main causative agents of hand, foot and mouth disease (HFMD). Unlike other enteroviruses that cause HFMD, EV-A71 is more frequently associated with severe neurological complications and fatality. To date, no effective licensed antivirals are available to combat EV-A71 infection. Little is known about the immunogenicity of viral non-structural proteins in humans. Previous studies have mainly focused on characterization of epitopes of EV-A71 structural proteins by using immunized animal antisera...
2016: PloS One
https://www.readbyqxmd.com/read/27788396/in-silico-analysis-of-hepatitis-c-virus-hcv-polyprotein-domains-and-their-comparison-with-other-pathogens-and-allergens-to-gain-insight-on-pathogenicity-mechanisms
#9
Seema Patel
Hepatitis C (HCV) is a deadly virus from family Flaviviridae, causing acute or chronic liver inflammation. Given its lethality and no known vaccine to curb it, understanding its pathogenic mechanism is critical. By analyzing the domains in its protein sequence, a plethora can be learnt about its immune manipulation strategies. In this regard, current in silico study compares publicly-available HCV polyprotein sequences and their domain profiles. Apart from using UniProt sequences and SMART (Simple modular architecture research tool) platform for domain profiling, a set of customized scripts were developed to extract the patterns of protein domain distribution...
October 15, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27787831/in-silico-prediction-of-linear-b-cell-epitopes-on-proteins
#10
Yasser El-Manzalawy, Drena Dobbs, Vasant G Honavar
Antibody-protein interactions play a critical role in the humoral immune response. B-cells secrete antibodies, which bind antigens (e.g., cell surface proteins of pathogens). The specific parts of antigens that are recognized by antibodies are called B-cell epitopes. These epitopes can be linear, corresponding to a contiguous amino acid sequence fragment of an antigen, or conformational, in which residues critical for recognition may not be contiguous in the primary sequence, but are in close proximity within the folded protein 3D structure...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27787680/identification-of-a-new-hepatitis-b-virus-recombinant-d2-d3-in-the-city-of-s%C3%A3-o-paulo-brazil
#11
Luiz Claudio Santana, Nathalia Pena Mantovani, Maira Cicero Ferreira, Rafael Arnold, Rodrigo Lopes Sanz Duro, Paulo Roberto Abrão Ferreira, James Richard Hunter, Élcio Leal, Ricardo Sobhie Diaz, Shirley Vasconcelos Komninakis
Two hundred forty million people are chronically infected with hepatitis B virus (HBV) worldwide. The rise of globalization has facilitated the emergence of novel HBV recombinants and genotypes. We evaluated HBV genotypes and recombinants, mutations associated with resistance to antivirals (AVs), progression of hepatic illness, and inefficient hepatitis B vaccination responses in chronically infected individuals in the city of São Paulo, Brazil. Forty-five full-length and 24 partial-length sequences were obtained...
October 27, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27778110/surface-proteome-mining-for-identification-of-potential-vaccine-candidates-against-campylobacter-jejuni-an-in-silico-approach
#12
Kusum Mehla, Jayashree Ramana
Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multifactorial in nature and not yet fully understood. Despite the completion of the first C. jejuni genome project in 2000, there are currently no vaccines in the market against this pathogen. Traditional vaccinology approach is an arduous and time extensive task...
October 24, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27769003/in-silico-identification-of-outer-membrane-protein-omp-and-subunit-vaccine-design-against-pathogenic-vibrio-cholerae
#13
Pradipta Ranjan Rauta, Sarbani Ashe, Debasis Nayak, Bismita Nayak
Virulence-related outer membrane proteins (Omps) are expressed in bacteria (Gram-negative) such as V. cholerae and are vital to bacterial invasion in to eukaryotic cell and survival within macrophages that could be best candidate for development of vaccine against V. cholerae. Applying in silico approaches, the 3-D model of the Omp was developed using Swiss model server and validated byProSA and Procheck web server. The continuous stretch of amino acid sequences 26mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds...
October 12, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27726597/analysis-of-coxiela-burnetti-dihydrofolate-reductase-via-in-silico-docking-with-inhibitors-and-molecular-dynamics-simulation
#14
Felipe Rodrigues de Souza, Ana Paula Guimarães, Teobaldo Cuya, Matheus Puggina de Freitas, Arlan da Silva Gonçalves, Pat Forgione, Tanos Celmar Costa França
Coxiella burnetii is a gram-negative bacterium able to infect several eukaryotic cells, mainly monocytes and macrophages. It is found widely in nature with ticks, birds, and mammals as major hosts. C. burnetii is also the biological warfare agent that causes Q fever, a disease that has no vaccine or proven chemotherapy available. Considering the current geopolitical context, this fact reinforces the need for discovering new treatments and molecular targets for drug design against C. burnetii. Among the main molecular targets against bacterial diseases reported, the enzyme dihydrofolate reductase (DHFR) has been investigated for several infectious diseases...
October 11, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27718189/in-silico-adjuvant-design-and-validation
#15
Matthew N Davies, Helene Pere, Iris Bosschem, Freddy Haesebrouck, Bram Flahou, Eric Tartour, Darren R Flower, David F Tough, Jagadeesh Bayry
Adjuvants are substances that boost the protective immune response to vaccine antigens. The majority of known adjuvants have been identified through the use of empirical approaches. Our aim was to identify novel adjuvants with well-defined cellular and molecular mechanisms by combining a knowledge of immunoregulatory mechanisms with an in silico approach. CD4(+)CD25(+)FoxP3(+) regulatory T cells (Tregs) inhibit the protective immune responses to vaccines by suppressing the activation of antigen presenting cells such as dendritic cells (DCs)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27667997/prediction-and-in-silico-identification-of-novel-b-cells-and-t-cells-epitopes-in-the-s1-spike-glycoprotein-of-m41-and-cr88-793-b-infectious-bronchitis-virus-serotypes-for-application-in-peptide-vaccines
#16
Faruku Bande, Siti Suri Arshad, Mohd Hair Bejo, Saeid Kadkhodaei, Abdul Rahman Omar
Bioinformatic analysis was used to predict antigenic B-cell and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. A conserved linear B-cell epitope peptide, YTSNETTDVTS(175-185), was identified in M41 IBV strains while three such epitopes types namely, VSNASPNSGGVD(279-290), HPKCNFRPENI(328-338), and NETNNAGSVSDCTAGT(54-69), were predicted in CR88 IBV strains. Analysis of MHCI binding peptides in M41 IBV strains revealed the presence of 15 antigenic peptides out of which 12 were highly conserved in 96-100% of the total M41 strains analysed...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27640170/designing-of-epitope-focused-vaccine-by-targeting-e6-and-e7-conserved-protein-sequences-an-immuno-informatics-approach-in-human-papillomavirus-58-isolates
#17
Sabrina Nusrat Sabah, Md Amran Gazi, Rahvia Alam Sthity, Amena Binte Husain, Salwa Abdul Quyyum, Mustafizur Rahman, Md Rezaul Islam
Human papillomavirus (HPV) is a DNA virus that belongs to the papillomavirus family and is capable of infecting humans. Currently, few vaccines are available to prevent infection by HPV. However, they are not so much effective and provide little benefit to women who have already been infected with HPV. The aim of this study was to design epitope-based vaccines of HPV58 by targeting E6 and E7 proteins of HPV58. Proteomic sequences were retrieved from different isolates at different time periods and later analyzed by performing alignment of these sequences...
September 17, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27633296/prediction-of-promiscuous-t-cell-epitopes-in-the-zika-virus-polyprotein-an-in-silico-approach
#18
Hamza Dar, Tahreem Zaheer, Muhammad Talha Rehman, Amjad Ali, Aneela Javed, Gohar Ayub Khan, Mustafeez Mujtaba Babar, Yasir Waheed
OBJECTIVE: To predict immunogenic promiscuous T cell epitopes from the polyprotein of the Zika virus using a range of bioinformatics tools. To date, no epitope data are available for the Zika virus in the IEDB database. METHODS: We retrieved nearly 54 full length polyprotein sequences of the Zika virus from the NCBI database belonging to different outbreaks. A consensus sequence was then used to predict the promiscuous T cell epitopes that bind MHC 1 and MHC II alleles using PorPred1 and ProPred immunoinformatic algorithms respectively...
September 2016: Asian Pacific Journal of Tropical Medicine
https://www.readbyqxmd.com/read/27625996/from-in-silico-protein-epitope-density-prediction-to-testing-escherichia-coli-o157-h7-vaccine-candidates-in-a-murine-model-of-colonization
#19
Daniel Tapia, Brittany N Ross, Anjana Kalita, Mridul Kalita, Christopher L Hatcher, Laura A Muruato, Alfredo G Torres
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a leading cause of foodborne illnesses worldwide and is a common serotype linked to hemorrhagic colitis and an important cause of hemolytic uremic syndrome (HUS). Treatment of EHEC O157:H7 infections is complicated, as antibiotics can exacerbate Shiga toxin (Stx) production and lead to more severe symptoms including HUS. To date, no vaccines have been approved for human use, exposing a void in both treatment and prevention of EHEC O157:H7 infections. Previously, our lab has shown success in identifying novel vaccine candidates via bio- and immunoinformatics approaches, which are capable of reducing bacterial colonization in an in vivo model of intestinal colonization...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27622028/current-tools-for-predicting-cancer-specific-t-cell-immunity
#20
REVIEW
David Gfeller, Michal Bassani-Sternberg, Julien Schmidt, Immanuel F Luescher
Tumor exome and RNA sequencing data provide a systematic and unbiased view on cancer-specific expression, over-expression, and mutations of genes, which can be mined for personalized cancer vaccines and other immunotherapies. Of key interest are tumor-specific mutations, because T cells recognizing neoepitopes have the potential to be highly tumoricidal. Here, we review recent developments and technical advances in identifying MHC class I and class II-restricted tumor antigens, especially neoantigen derived MHC ligands, including in silico predictions, immune-peptidome analysis by mass spectrometry, and MHC ligand validation by biochemical methods on T cells...
July 2016: Oncoimmunology
keyword
keyword
59884
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"