title: In silico study of rotavirus VP7 surface accessible conserved regions for antiviral drug/vaccine design.
abstract: BACKGROUND
  Rotaviral diarrhoea kills about half a million children annually in developing countries and accounts for one third of diarrhea related hospitalizations. Drugs and vaccines against the rotavirus are handicapped, as in all viral diseases, by the rapid mutational changes that take place in the DNA and protein sequences rendering most of these ineffective. As of now only two vaccines are licensed and approved by the WHO (World Health Organization), but display reduced efficiencies in the underdeveloped countries where the disease is more prevalent. We approached this issue by trying to identify regions of surface exposed conserved segments on the surface glycoproteins of the virion, which may then be targeted by specific peptide vaccines. We had developed a bioinformatics protocol for these kinds of problems with reference to the influenza neuraminidase protein, which we have refined and expanded to analyze the rotavirus issue.
  
  
  RESULTS
  Our analysis of 433 VP7 (Viral Protein 7 from rotavirus) surface protein sequences across 17 subtypes encompassing mammalian hosts using a 20D Graphical Representation and Numerical Characterization method, identified four possible highly conserved peptide segments. Solvent accessibility prediction servers were used to identify that these are predominantly surface situated. These regions analyzed through selected epitope prediction servers for their epitopic properties towards possible T-cell and B-cell activation showed good results as epitopic candidates (only dry lab confirmation).
  
  
  CONCLUSIONS
  The main reasons for the development of alternative vaccine strategies for the rotavirus are the failure of current vaccines and high production costs that inhibit their application in developing countries. We expect that it would be possible to use the protein surface exposed regions identified in our study as targets for peptide vaccines and drug designs for stable immunity against divergent strains of the rotavirus. Though this study is fully dependent on computational prediction algorithms, it provides a platform for wet lab experiments.
authors: Physics Department, Jadavpur University, Kolkata, West Bengal, India.
authors: Ambarnil
authors: A
authors: Ghosh
authors: Shiladitya
authors: S
authors: Chattopadhyay
authors: Mamta
authors: M
authors: Chawla-Sarkar
authors: Papiya
authors: P
authors: Nandy
authors: Ashesh
authors: A
authors: Nandy
mesh_terms: D000818:Animals; D000956:Antigens, Viral / Q000737:chemistry* / Q000276:immunology*; D000998:Antiviral Agents / Q000494:pharmacology; D036022:Capsid Proteins / Q000737:chemistry* / Q000276:immunology*; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D017124:Conserved Sequence; D015195:Drug Design; D000939:Epitopes / Q000276:immunology; D008958:Models, Molecular; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D012401:Rotavirus / Q000187:drug effects / Q000276:immunology*; D014765:Viral Vaccines / Q000276:immunology*
chemical_list: D000956:Antigens, Viral; D000998:Antiviral Agents; D036022:Capsid Proteins; D000939:Epitopes; C050779:VP7 protein, Rotavirus; D014765:Viral Vaccines