In silico Prediction and Evaluation of Human Parainfluenza Virus-3 CD4⁺ T Cell Epitopes

Background Human parainfluenza viruses type 3 (HPIV-3) through bronchiolitis and pneumonia is a common cause of lower respiratory tract infections. It is the main cause of hospitalization of infants and young children and also one of the main causes of morbidity and mortality in immuno-compromised and transplant patients. Despite many efforts, there is currently no specific anti-HPIV-3 drug or approved vaccine to prevent and control the virus. Identification of HPIV-3 epitopes with the capability of binding to human leukocyte antigen (HLA) class II molecules can be helpful in designing new vaccine candidates against HPIV-3 infection, and also can be useful for the in vitro stimulation and proliferation of HPIV-3-specific T cells for transplant and immunocompromised patients. Objective To predict and comprehensively evaluate CD4(+)T cell epitope (HLA-II binders) from four main HPIV-3 antigens. Methods In the present work, we predicted and comprehensively evaluated CD4(+)T cell epitope (HLA-II binders) from four main HPIV-3 antigens, including fusion protein (F), hemagglutinin-neuraminidase (HN), nucleocapsid (N) and matrix (M) proteins using bio- and immuno-informatics software. The toxicity, allergenicity, Blast screening and population coverage of the predicted epitopes were evaluated. The binding ability of the final selected epitopes was evaluated via a docking study. Results After several filtering steps, including blast screening, toxicity and allergenicity assay, population coverage and docking study, 9 epitopes were selected as candidate epitopes. The selected epitopes showed high population coverage and docking studies revealed a significantly higher binding affinity for the final epitopes in comparison with the negative control peptides. Conclusion The final selected epitopes could be useful in designing vaccine candidates and for the treatment of immune-compromised individuals and patients with transplantation.