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Srivastava M.,Society for Biological Research and Rural Development | Akhoon B.A.,Jammu University | Gupta S.K.,Society for Biological Research and Rural Development | Gupta S.K.,Indian Institute of Toxicology Research
Fungal Genetics and Biology | Year: 2010

Blackleg caused by Leptosphaeria maculans is a very important disease worldwide and causes large yield loss of significant vegetable crops of Brassicaceae family. Absence of resistant 'B' genome in vegetable Brassica oleracea proposed these species susceptible to blackleg disease. We present a specific piece of molecular modelling work, combining in silico docking methods, energy minimization calculations and in silico cloning, to develop a rational peptide as a candidate that functions as a resistance inducing agent against L. maculans in B. oleracea var. botrytis. These studies are based upon predicted interaction sites of isocitrate lyase (ICL) and isocitrate. Inhibition of isocitrate binding to ICL is demonstrated to prevent rescue of glyoxylate cycle that is essential for metabolism of L. maculans in B. oleracea. We have taken the predicted interaction domain from the isocitrate lyase enzyme and randomly generated the best fitting 9-amino acid peptide among various screened peptides. © 2010 Elsevier Inc.

Gupta S.K.,University of Heidelberg | Srivastava M.,Society for Biological Research and Rural Development | Akhoon B.A.,Indian Institute of Toxicology Research | Gupta S.K.,Indian Institute of Toxicology Research | Grabe N.,University of Heidelberg
Infection, Genetics and Evolution | Year: 2012

Primary approach to prevent cervical cancer includes the development of human papillomavirus (HPV) vaccines. Currently available HPV vaccines (Gardasil and Cervarix) predominantly consider HPV16 and HPV18 strains. However, due to ignorance of the other high-risk strains aside from HPV16 and HPV18 during vaccine development, the critical need is to synthesize a vaccine with possible protection against all the high-risk HPV types. One feasible approach is to design a vaccine containing conserved immunogenic peptides that represent the genotypic diversity of all the current and future high-risk HPV types. While the epitopes derived from sequentially conserved regions may undergo mutations, it is worthwhile to explore the structurally conserved regions as a new dimension for epitope prediction. In the present study, 81 structurally conserved peptides were predicted to have immune relevance as T-cell epitopes of all the reported high-risk HPV proteins studied. A small dataset of three epitopes was also recognized as potential vaccine candidates generating both CD8+ and CD4+ responses. © 2012 Elsevier B.V.

Gupta S.K.,Society for Biological Research and Rural Development | Srivastava M.,Society for Biological Research and Rural Development | Akhoon B.A.,Jammu University | Smita S.,Integral University | And 5 more authors.
Infection, Genetics and Evolution | Year: 2011

Antigenic drift is the ability of the swine influenza virus to undergo continuous and progressive changes in response to the host immune system. These changes dictate influenza vaccine updates annually to ensure inclusion of antigens of the most current strains. The identification of those peptides that stimulate T-cell responses, termed T-cell epitopes, is essential for the development of successful vaccines. In this study, the highly conserved and specific epitopes from neuraminidase of globally distributed H1N1 strains were predicted so that these potential vaccine candidates may escape with antigenic drift. A total of nine novel CD8 + T-cell epitopes for MHC class-I and eight novel CD4 + T-cell epitopes for MHC class-II alleles were proposed as novel epitope based vaccine candidates. Additionally, the epitope FSYKYGNGV was identified as a highly conserved, immunogenic and potential vaccine candidate, capable for generating both CD8 + and CD4 + responses. © 2010 Elsevier B.V.

Gupta S.K.,Society for Biological Research and Rural Development | Smita S.,Integral University | Sarangi A.N.,Sanjay Gandhi Post Graduate Institute of Medical Sciences | Srivastava M.,Society for Biological Research and Rural Development | And 3 more authors.
Vaccine | Year: 2010

Neisseria meningitidis, an exclusive human pathogen, is a major cause of mortality due to meningococcal meningitis and sepsis in many developing countries. Three meningococcal serogroup B proteins, i.e. T-cell stimulating protein A (TspA), autotransporter A (AutA), and IgA-specific serine endopeptidase (IGA1) elicits CD4+ T-cell response and may enhance the effectiveness of meningococcal vaccines by acting as protective immunogens. A very limited data on T-helper cell epitopes in MenB proteins is available. Hence, in silico prediction of peptide sequences which may act as helper T lymphocyte epitopes in MenB proteins was carried out by NetMHCIIpan web server. HLA distribution analysis was done by using the population coverage tool of Immune Epitope Database to determine the fraction of individuals in various populations expected to respond to a given set of predicted T-cell epitopes based on HLA genotype frequencies. Six epitopic core sequences, two from each MenB proteins, i.e. AutA, TspA and IgA1 protease were predicted to associate with a large number of HLA-DR alleles. These six peptides may act as T-cell epitope in more than 95% of populations in 8 out of 12 populations considered. The T-cell stimulation potential of these predicted peptides containing the core epitopic sequences is to be validated by using laboratory experiments for their efficient use as peptide vaccine candidates against N. meningitidis serogroup B. © 2010 Elsevier Ltd.

Baloria U.,Shri Mata Vaishno Devi University | Akhoon B.A.,Shri Mata Vaishno Devi University | Gupta S.K.,Society for Biological Research and Rural Development | Sharma S.,Indian Institute of Integrative Medicine | Verma V.,Shri Mata Vaishno Devi University
Amino Acids | Year: 2012

Multiple different approaches are being used to activate the immune system against breast cancer. Vaccine therapy in general follows the principle that injections of various substances ultimately result in the presentation of tumor peptides to the patient's immune system. We proposed a potential in silico DNA vaccine against breast cancer by integrating high affinity T cell (MHC-I and MHCII) and B cell (continuous and discontinuous) epitopes. The matching of the HLA haplotype and antigen was performed to provide the appropriate peptide epitope suitable for majority of the patients. The immunogenic nature of the antigenic construct was also enhanced by the administration of consensus epitopes. The potency of DNA vaccines depends on the efficient expression and presentation of the encoded antigen of interest and the chances of efficient expression of our antigenic construct in host organism was also verified by in silico approaches. An attempt was made to overcome the limited potency of the DNA vaccine by targeting DNA to professional antigen-presenting cells (APCs). A higher immune response theoretically corresponds to a higher survival rate of patients. Therefore, optimization studies were also employed to enhance the immunogenicity of proposed in silico DNA vaccine. © Springer-Verlag 2011.

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