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In silico vaccine

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https://www.readbyqxmd.com/read/28932628/a-novel-in-silico-framework-to-improve-mhc-i-epitopes-and-break-the-tolerance-to-melanoma
#1
Cristian Capasso, Aniket Magarkar, Victor Cervera-Carascon, Manlio Fusciello, Sara Feola, Martin Muller, Mariangela Garofalo, Lukasz Kuryk, Siri Tähtinen, Lucio Pastore, Alex Bunker, Vincenzo Cerullo
Tolerance toward tumor antigens, which are shared by normal tissues, have often limited the efficacy of cancer vaccines. However, wild type epitopes can be tweaked to activate cross-reactive T-cell clones, resulting in antitumor activity. The design of these analogs (i.e., heteroclitic peptides) can be difficult and time-consuming since no automated in silico tools are available. Hereby we describe the development of an in silico framework to improve the selection of heteroclitic peptides. The Epitope Discovery and Improvement System (EDIS) was first validated by studying the model antigen SIINFEKL...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28932211/strain-level-streptococcus-colonization-patterns-during-the-first-year-of-life
#2
Meredith S Wright, Jamison McCorrison, Andres M Gomez, Erin Beck, Derek Harkins, Jyoti Shankar, Stephanie Mounaud, Edelwisa Segubre-Mercado, Aileen May R Mojica, Brian Bacay, Susan A Nzenze, Sheila Z M Kimaro, Peter Adrian, Keith P Klugman, Marilla G Lucero, Karen E Nelson, Shabir Madhi, Granger G Sutton, William C Nierman, Liliana Losada
Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28929019/heterologous-expression-of-plasmodium-vivax-apical-membrane-antigen-1-pvama1-for-binding-peptide-selection
#3
Ching Hoong Chew, Yvonne Ai Lian Lim, Kek Heng Chua
BACKGROUND: Plasmodium is an obligate intracellular parasite. Apical membrane antigen 1 (AMA1) is the most prominent and well characterized malarial surface antigen that is essential for parasite-host cell invasion, i.e., for sporozoite to invade and replicate within hepatocytes in the liver stage and merozoite to penetrate and replicate within erythrocytes in the blood stage. AMA1 has long served as a potent antimalarial drug target and is a pivotal vaccine candidate. A good understanding of the structure and molecular function of this Plasmodium protein, particularly its involvement in host-cell adhesion and invasion, is of great interest and hence it offers an attractive target for the development of novel therapeutics...
2017: PeerJ
https://www.readbyqxmd.com/read/28928941/computational-design-of-molecular-motors-as-nanocircuits-in-leishmaniasis
#4
Dipali Kosey, Shailza Singh
Cutaneous leishmaniasis is the most common form of leishmaniasis, caused by Leishmania major and is spread by the bite of a sandfly .This species infects the macrophages and dendritic cells Due to multi-drug resistance, there is a need for a new therapeutic technique. Recently, a novel molecular motor of Leishmania, Myosin XXI, was classified and characterized. In addition, the drug resistance in this organism has been linked with the overexpression of ABC transporters. Systems biology aims to study the simulation and modeling of natural biological systems whereas synthetic biology deals with building novel and artificial biological parts and devices  Together they have contributed enormously to drug discovery, vaccine design and development, infectious disease detection and diagnostics...
2017: F1000Research
https://www.readbyqxmd.com/read/28923896/experimental-and-theoretical-approaches-to-investigate-the-immunogenicity-of-taenia-solium-derived-ke7-antigen
#5
Raúl J Bobes, José Navarrete-Perea, Adrián Ochoa-Leyva, Víctor Hugo Anaya, Marisela Hernández, Jacquelynne Cervantes-Torres, Karel Estrada, Filiberto Sánchez-Lopez, Xavier Soberón, Gabriela Rosas, Cáris Maroni Nunes, Martín García-Varela, Rogerio Rafael Sotelo-Mundo, Alonso Alexis López-Zavala, Goar Gevorkian, Gonzalo Acero, Juan P Laclette, Gladis Fragoso, Edda Sciutto
Taenia solium cysticercosis, a parasitic disease that affects human health in various regions of the world, is preventable by vaccination. Both the 97-amino-acid-long KETc7 peptide and its carboxyl-terminal, 18-amino-acid-long sequence (GK-1) are found in Taenia crassiceps Both peptides, with proven protective capacity against cysticercosis, are part of the highly conserved, cestode-native, 264-amino-acid long protein KE7. KE7 belongs to a ubiquitously distributed family of proteins associated to membrane processes and may participate in several vital cell pathways...
September 18, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28906178/comparison-of-whole-genome-sequencing-to-restriction-endonuclease-analysis-and-gel-diffusion-precipitin-based-serotyping-of-pasteurella-multocida
#6
Karen J LeCount, Linda K Schlater, Tod Stuber, Suelee Robbe Austerman, Timothy S Frana, Ronald W Griffith, Matthew M Erdman
The gel diffusion precipitin test (GDPT) and restriction endonuclease analysis (REA) have commonly been used in the serotyping and genotyping of Pasteurella multocida. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis has become the gold standard for other organisms, offering higher resolution than previously available methods. We compared WGS to REA and GDPT on 163 isolates of P. multocida to determine if WGS produced more precise results. The isolates used represented the 16 reference serovars, isolates with REA profiles matching an attenuated fowl cholera vaccine strain, and isolates from 10 different animal species...
September 1, 2017: Journal of Veterinary Diagnostic Investigation
https://www.readbyqxmd.com/read/28903988/the-use-of-reverse-vaccinology-in-the-design-and-construction-of-nano-glycoconjugate-vaccines-against-burkholderia-pseudomallei
#7
Laura A Muruato, Daniel Tapia, Christopher L Hatcher, Mridul Kalita, Paul J Brett, Anthony E Gregory, James E Samuel, Richard W Titball, Alfredo G Torres
Burkholderia pseudomallei (Bpm) is a Gram negative, facultative intracellular pathogen that causes the disease melioidosis in humans and other mammals. Respiratory infection with B. pseudomallei leads to a fulminant and often fatal disease. It has previously been shown that glycoconjugate vaccines can provide significant protection against lethal challenge; however, the limited number of known Burkholderia antigens has slowed progress towards vaccine development. The objective of this study was to identify novel antigens and evaluate their protective capacity when incorporated into a nano-glycoconjugate vaccine platform...
September 13, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/28894200/soluble-hla-associated-peptide-from-psf1-has-a-cancer-vaccine-potency
#8
Mari Yoshida, Yukichi Ishioka, Takamasa Ozawa, Hirohisa Okuyama, Motofumi Iguchi, Takeshi Ota, Takaomi Ito, Morio Nagira, Atsushi Morita, Hidekazu Tanaka, Hisamichi Naito, Hiroyasu Kidoya, Nobuyuki Takakura
Partner of sld five 1 (PSF1) is an evolutionary conserved DNA replication factor involved in DNA replication in lower species, which is strongly expressed in normal stem cell populations and progenitor cell populations. Recently, we have investigated PSF1 functions in cancer cells and found that PSF1 plays a significant role in tumour growth. These findings provide initial evidence for the potential of PSF1 as a therapeutic target. Here, we reveal that PSF1 contains an immunogenic epitope suitable for an antitumour vaccine...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28893639/on-the-application-of-reverse-vaccinology-to-parasitic-diseases-a-perspective-on-feature-selection-and-ranking-of-vaccine-candidates
#9
Stephen J Goodswen, Paul J Kennedy, John T Ellis
Reverse vaccinology has the potential to rapidly advance vaccine development against parasites, but it is unclear which features studied in silico will advance vaccine development. Here we consider Neospora caninum which is a globally distributed protozoan parasite causing significant economic and reproductive loss to cattle industries worldwide. The aim of this study was to use a reverse vaccinology approach to compile a worthy vaccine candidate list for N. caninum, including proteins containing pathogen-associated molecular patterns to act as vaccine carriers...
September 8, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28886485/development-of-an-epitope-based-vaccine-inhibiting-immune-cells-rolling-and-migration-against-atherosclerosis-using-in-silico-approaches
#10
Mehdi Tourani, Ahmad Karkhah, Ali Najafi
Atherosclerosis is a chronic inflammatory disease characterized by formation of pro-oxidative lipids in large and medium-sized vessels. Over the years, many treatments and drugs have entered the market to improve atherosclerosis and autoantigen-mediated active immunization is currently considered as a beneficial method. Therefore, this study was conducted to design a novel epitope-based vaccine against atherosclerosis employing CD99, CD81 and CD99L2 antigens. In this way, structural vaccinology approaches were used to design a novel multi-epitope vaccine against atherosclerosis...
September 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28856362/an-immunoinformatics-approach-to-promiscuous-peptide-design-for-the-plasmodium-falciparum-erythrocyte-membrane-protein-1
#11
Nazam Khan, Rajender Kumar, Shakti Chauhan, Umar Farooq
Plasmodium falciparum erythrocyte membrane protein-1 (Pfemp-1), a variant adhesion molecule, can act as a key component of immunity against malaria. In the current selection of malaria vaccines, no efficient vaccines are available that can be employed for its proper treatment. Unfortunately, resistance to post-infection treatments is increasing and therefore there is a pressing need to develop an efficient vaccine. Peptide-based vaccines can be effective tools against malaria but HLA restriction is a major hindrance which can be conquered by using promiscuous peptides...
August 31, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28835708/exploring-dengue-genome-to-construct-a-multi-epitope-based-subunit-vaccine-by-utilizing-immunoinformatics-approach-to-battle-against-dengue-infection
#12
Mudassar Ali, Rajan Kumar Pandey, Nazia Khatoon, Aruna Narula, Amit Mishra, Vijay Kumar Prajapati
Dengue is considered as a major health issue which causes a number of deaths worldwide each year; tropical countries are majorly affected by dengue outbreaks. It is considered as life threatening issue because, since many decades not a single effective approach for treatment and prevention of dengue has been developed. Therefore, to find new preventive measure, we used immunoinformatics approaches to develop a multi-epitope based subunit vaccine for dengue which can generate various immune responses inside the host...
August 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28834304/sofosbuvir-as-treatment-against-dengue
#13
Chye Sheng Gan, See Khai Lim, Chin Fei Chee, Rohana Yusof, Choon Han Heh
Dengvaxia(®) (CTD-TDV), the only licensed tetravalent dengue vaccine by Sanofi Pasteur was made available since 2015. However, administration of CTD-TDV in general has not received the prequalification recommendation from the World Health Organization. Having a universal anti-dengue agent for treatment will therefore beneficial. Accordingly, the development of nucleoside inhibitors specific to dengue viral polymerase that perturb dengue infection has been studied by many. Alternatively, we have used a marketed anti-HCV prodrug sofosbuvir to study it's in silico and in vitro effects against dengue...
August 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28795601/poly-glutamic-dendrimer-based-conjugates-for-cancer-vaccination-a-computational-design-for-targeted-delivery-of-antigens
#14
L I F Moura, N Martinho, L C Silva, T S Barata, S Brocchini, H F Florindo, M Zloh
Computational techniques are useful to predict interaction models and molecular properties for the design of drug delivery systems, such as dendrimers. This work evaluated the impact of surface modifications of mannosamine-conjugated multifunctional poly(glutamic acid) (PG)-dendrimers as nanocarriers of the tumour associated antigens (TAA) MART-1, gp100:44 and gp100:209. Molecular dynamics simulations and docking studies were performed. Nitrobenzoxadiazole (NBD)-PG-G4-dendrimer displayed 64 carboxylic groups, however, the Frontier Molecular Orbital Theory study evidenced that only 32 of those were available to form covalent bonds...
August 10, 2017: Journal of Drug Targeting
https://www.readbyqxmd.com/read/28767653/in-silico-analysis-to-identify-vaccine-candidates-common-to-multiple-serotypes-of-shigella-and-evaluation-of-their-immunogenicity
#15
Sapna Pahil, Neelam Taneja, Hifzur Rahman Ansari, G P S Raghava
Shigellosis or bacillary dysentery is an important cause of diarrhea, with the majority of the cases occurring in developing countries. Considering the high disease burden, increasing antibiotic resistance, serotype-specific immunity and the post-infectious sequelae associated with shigellosis, there is a pressing need of an effective vaccine against multiple serotypes of the pathogen. In the present study, we used bio-informatics approach to identify antigens shared among multiple serotypes of Shigella spp...
2017: PloS One
https://www.readbyqxmd.com/read/28756915/in-silico-identification-and-characterization-of-common-epitope-based-peptide-vaccine-for-nipah-and-hendra-viruses
#16
Chayan Kumar Saha, Md Mahbub Hasan, Md Saddam Hossain, Md Asraful Jahan, Abul Kalam Azad
OBJECTIVE: To explore a common B- and T-cell epitope-based vaccine that can elicit an immune response against encephalitis causing genus Henipaviruses, Hendra virus (HeV) and Nipah virus (NiV). METHODS: Membrane proteins F, G and M of HeV and NiV were retrieved from the protein database and subjected to different bioinformatics tools to predict antigenic B-cell epitopes. Best B-cell epitopes were then analyzed to predict their T-cell antigenic potentiality. Antigenic B- and T-cell epitopes that shared maximum identity with HeV and NiV were selected...
June 2017: Asian Pacific Journal of Tropical Medicine
https://www.readbyqxmd.com/read/28740150/identification-of-putative-unique-immunogenic-zikv-and-denv1-4-peptides-for-diagnostic-cellular-based-tests
#17
Aaron L Oom, Davey Smith, Kevan Akrami
Since the re-emergence of Zika virus in 2014 and subsequent association with microcephaly, much work has focused on the development of a vaccine to halt its spread throughout the world. The mosquito vector that transmits this virus is widespread and responsible for the spread of other arboviridae including Dengue. Current diagnostic methods rely on serologic testing that are complicated by cross reactivity and therefore unable to distinguish Zika from Dengue infection in the absence of virus isolation. We performed an in silico analysis to identify potential epitopes that may stimulate a unique T-lymphocyte response to distinguish prior infection with Zika or Dengue...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28734965/enhanced-immunostimulatory-activity-of-in-silico-discovered-agonists-of-toll-like-receptor-2-tlr2
#18
M S Murgueitio, S Ebner, P Hörtnagl, C Rakers, R Bruckner, P Henneke, G Wolber, S Santos-Sierra
BACKGROUND: Emergent therapies in anticancer vaccination use Toll-like receptors (TLRs) agonists as dendritic cell (DC) vaccine adjuvants. DCs from the patient are isolated, stimulated with TLR agonists and tumor antigens ex vivo and then infused back into the patient. Although some TLR ligands have been tested in clinical trials, novel TLR agonists with improved immunomodulatory properties are essential to optimize treatment success. We report on the discovery of small-molecule TLR2 agonists, with favorable properties as synthetic adjuvants...
July 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28717032/th17-mediated-cross-protection-against-pneumococcal-carriage-by-vaccination-with-a-variable-antigen
#19
Kirsten Kuipers, Wouter S P Jong, Christa E van der Gaast-de Jongh, Diane Houben, Fred van Opzeeland, Elles Simonetti, Saskia van Selm, Ronald de Groot, Marije I Koenders, Taj Azarian, Elder Pupo, Peter van der Ley, Jeroen D Langereis, Aldert Zomer, Joen Luirink, Marien I de Jonge
Serotype-specific protection against a Streptococcus pneumoniae is an important limitation of the current polysaccharide-based vaccines. To prevent serotype replacement, reduce transmission and limit emergence of new variants, it is essential to induce broad protection and restrict pneumococcal colonization. In this study, we used a prototype vaccine formulation consisting of LPS-detoxified outer membrane vesicles (OMVs) from Salmonella Typhimurium displaying the variable N-terminus of PspA (α1α2) for intranasal vaccination, which induced strong Th17 immunity associated with substantial reduction of pneumococcal colonization...
July 17, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28674640/in-silico-prediction-and-modeling-of-the-entamoeba-histolytica-proteins-serine-rich-entamoeba-histolytica-protein-and-29%C3%A2-kda-cysteine-rich-protease
#20
Kumar Manochitra, Subhash Chandra Parija
BACKGROUND: Amoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic approach. Serine-rich Entamoeba histolyticaprotein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal in E. histolyticavirulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential...
2017: PeerJ
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