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In silico vaccine

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
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
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
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
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
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
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
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
Rafael de Freitas E Silva, Luiz Felipe Gomes Rebello Ferreira, Marcelo Zaldini Hernandes, Maria Edileuza Felinto de Brito, Beatriz Coutinho de Oliveira, Ailton Alvaro da Silva, Osvaldo Pompílio de-Melo-Neto, Antônio Mauro Rezende, Valéria Rêgo Alves Pereira
The leishmaniases are neglected tropical diseases widespread throughout the globe, which are caused by protozoans from the genus Leishmania and are transmitted by infected phlebotomine flies. The development of a safe and effective vaccine against these diseases has been seen as the best alternative to control and reduce the number of cases. To support vaccine development, this work has applied an in silico approach to search for high potential peptide epitopes able to bind to different major histocompatibility complex Class I and Class II (MHC I and MHC II) molecules from different human populations...
2016: Frontiers in Immunology
Ravi Jain, Subash C Sonkar, Uma Chaudhry, Manju Bala, Daman Saluja
OBJECTIVES: Resistance to the currently recommended extended-spectrum cephalosporins, which is used to treat Gonorrhea, is increasing continuously and leading to a threat of untreatable infection. It is, therefore, becoming extremely essential to search for new therapeutic strategies to control Gonorrhea. Vaccination may be considered as an effective control measure to control this disease, which is caused by Neisseria gonorrhoeae. METHODS: In-silico hierarchical approach was used to help identify candidate proteins of N...
September 3, 2016: Journal of Theoretical Biology
Mohammad Nouh Issa, Yaqoub Ashhab
Brucella melitensis Rev.1 is an avirulent strain that is widely used as a live vaccine to control brucellosis in small ruminants. Although an assembled draft version of Rev.1 genome has been available since 2009, this genome has not been investigated to characterize this important vaccine. In the present work, we used the draft genome of Rev.1 to perform a thorough genomic comparison and sequence analysis to identify and characterize the panel of its unique genetic markers. The draft genome of Rev.1 was compared with genome sequences of 36 different Brucella melitensis strains from the Brucella project of the Broad Institute of MIT and Harvard...
September 22, 2016: Vaccine
Anouk C M Platteel, A Marit de Groot, Christin Keller, Peter Andersen, Huib Ovaa, Peter M Kloetzel, Michele Mishto, Alice J A M Sijts
Most vaccines are based on protective humoral responses while for intracellular pathogens CD8(+) T cells are regularly needed to provide protection. However, poor processing efficiency of antigens is often a limiting factor in CD8(+) T cell priming, hampering vaccine efficacy. The multistage cDNA vaccine H56, encoding three secreted Mycobacterium tuberculosis antigens, was used to test a complete strategy to enhance vaccine' immunogenicity. Potential CD8(+) T cell epitopes in H56 were predicted using the NetMHC3...
September 30, 2016: Vaccine
Kendall G Byler, Ifedayo Victor Ogungbe, William N Setzer
Zika virus (ZIKV) is an arbovirus that has infected hundreds of thousands of people and is a rapidly expanding epidemic across Central and South America. ZIKV infection has caused serious, albeit rare, complications including Guillain-Barré syndrome and congenital microcephaly. There are currently no vaccines or antiviral agents to treat or prevent ZIKV infection, but there are several ZIKV non-structural proteins that may serve as promising antiviral drug targets. In this work, we have carried out an in-silico search for potential anti-Zika viral agents from natural sources...
September 2016: Journal of Molecular Graphics & Modelling
Duane H Hamilton, Mario Roselli, Patrizia Ferroni, Leopoldo Costarelli, Francesco Cavaliere, Mariateresa Taffuri, Claudia Palena, Fiorella Guadagni
Patients diagnosed with triple-negative breast cancer (TNBC) have a high rate of tumor metastasis and a poor prognosis. The treatment option for these patients is currently chemotherapy, which results in very low response rates. Strategies that exploit the immune system for the treatment of cancer have now shown the ability to improve survival in several tumor types. Identifying potential targets for immune therapeutic interventions is an important step in developing novel treatments for TNBC. In this study, in silico analysis of publicly available datasets and immunohistochemical analysis of primary and metastatic tumor biopsies from TNBC patients were conducted to evaluate the expression of the transcription factor brachyury, which is a driver of tumor metastasis and resistance and a target for cancer vaccine approaches...
October 2016: Endocrine-related Cancer
Jingxuan Qiu, Tianyi Qiu, Yiyan Yang, Dingfeng Wu, Zhiwei Cao
The rapid and consistent mutation of influenza requires frequent evaluation of antigenicity variation among newly emerged strains, during which several in-silico methods have been reported to facilitate the assays. In this paper, we designed a structure-based antigenicity scoring model instead of those sequence-based previously published. Protein structural context was adopted to derive the antigenicity-dominant positions, as well as the physic-chemical change of local micro-environment in correlation with antigenicity change...
2016: Scientific Reports
Karina Juhl Rasmussen, Andreas Holm Mattsson, Katrine Pilely, Cecilie Antoinette Asferg, Oana Ciofu, Lars Vitved, Claus Koch, Michael Kemp
Methicillin-resistant Staphylococcus aureus (MRSA) is a rapidly growing problem, especially in hospitals where MRSA cause increased morbidity and mortality and a significant rise in health expenditures. As many strains of MRSA are resistant to other antimicrobials in addition to methicillin, there is an urgent need to institute non-antimicrobial measures, such as vaccination, against the spread of MRSA. With the aim of finding new protective antigens for vaccine development, this study used a proteome-wide in silico antigen prediction platform to screen the proteome of S...
August 31, 2016: Vaccine
Drista Sharma, Rani Soni, Sachin Patel, Deepti Joshi, Tarun Kumar Bhatt
Despite encouraging progress over the past decade, malaria caused by the Plasmodium parasite continues to pose an enormous disease burden and is one of the major global health problems. The extreme challenge in malaria management is the resistance of parasites to traditional monochemotherapies like chloroquine and sulfadoxine-pyrimethamine. No vaccine is yet in sight, and the foregoing effective drugs are also losing ground against the disease due to the resistivity of parasites. New antimalarials with novel mechanisms of action are needed to circumvent existing or emerging drug resistance...
September 2016: Journal of Molecular Modeling
Aftab Alam, Shahnwaz Ali, Shahzaib Ahamad, Md Zubbair Malik, Romana Ishrat
Recently, Zika virus has emerged as a potential threat to human health worldwide. Zika is the member of Flaviviridae, is transmitted to humans by mosquitoes. It is related to other pathogenic vector borne flaviviruses including dengue, West-Nile and Japanese encephalitis viruses, but produces a comparatively mild disease in humans. Despite of its epidemic outbreak and lack of potential medication, there is a need for improved vaccine /drugs. The use of computational technique will bring some facts into the research limelight...
August 3, 2016: Immunology
Kyle Saylor, Chenming Zhang
Physiologically based pharmacokinetic (PBPK) modeling was applied to investigate the effects of anti-nicotine antibodies on nicotine disposition in the brains of rats and humans. Successful construction of both rat and human models was achieved by fitting model outputs to published nicotine concentration time course data in the blood and in the brain. Key parameters presumed to have the most effect on the ability of these antibodies to prevent nicotine from entering the brain were selected for investigation using the human model...
September 15, 2016: Toxicology and Applied Pharmacology
Masatoshi Hirayama, Yusuke Tomita, Akira Yuno, Hirotake Tsukamoto, Satoru Senju, Yuya Imamura, Mohammad Abu Sayem, Atsushi Irie, Yoshihiro Yoshitake, Daiki Fukuma, Masanori Shinohara, Akinobu Hamada, Hirofumi Jono, Eiji Yuba, Kenji Kono, Koji Yoshida, Takuya Tsunoda, Hideki Nakayama, Yasuharu Nishimura
Insulin-like growth factor II mRNA-binding protein 3 (IMP-3), an oncofetal antigen identified using genome-wide cDNA microarray analyses, is overexpressed in several malignancies. IMP-3-derived cytotoxic T lymphocyte (CTL) epitopes have been used for peptide-based immunotherapies against various cancers. In addition to CTLs, induction of tumor-associated antigen (TAA)-specific helper T (Th) cells is crucial for establishment of effective antitumor immunity. In this study, we aimed to identify IMP-3-derived long peptides (IMP-3-LPs) carrying CTL and promiscuous Th-cell epitopes for use in cancer immunotherapy...
June 2016: Oncoimmunology
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