Integration of in-silico approaches for designing b cell epitopes for disease diagnosis

In this technologically savvy world, we witness mushrooming of sophisticated line of softwares that are extensively used for predicting epitopes towards developing vaccines and therapeutics. However, most softwares also generate bulky junk data along with data of interest. Here we devised a combined usage of B cell epitope prediction softwares- ABCpred along with additional online tools such as CLUSTAL W and Sequence Manipulation Suite for stringent selection of B cell epitopes. Dengue was used as model disease since the present diagnostic kits give false positives owing to cross-reactivity with other flaviviruses. The in silico predicted 240 unique B cell epitopes of dengue viruses were reduced to 87 serotype-specific epitopes using combination of softwares. Three best ranking epitopes of each dengue serotype were functionally validated by cloning corresponding DNA sequences in thep CBP vector and expressing these epitopes as calcium-binding protein fusion proteins. Western blot analysis and indirect ELISAs of purified fusion proteins confirmed that nearly fifty percent of the epitopes were in close agreement with the predictions.Thus, stringent selection of epitopes using a combination of prediction softwares is likely to identify a compact library of B cell epitopes useful for developing more specific diagnostics in future.