Antibody epitope and mimotope prediction of the viroporins M2 of the Influenza A virus, E of the Human SARS coronavirus and SH of the Respiratory Syncytial virus

Abstract

<b>Background:</b> Viroporins, such as the Matrix protein 2 (M2) of the Influenza A virus, the Envelope small membrane protein (E) of the Human SARS coronavirus, and the SH protein of the Respiratory Syncytial virus, are integral membrane proteins with ion channel activity. Viroporins have been associated with pathogenesis and virulence thus representing possible targets for antivirals. <b>Objectives:</b> In this study, we focused on the prediction of linear B cells epitopes from the M2, E and SH sequences. Moreover, we aimed at retrieving mimotopes for the specific epitopes. <b>Methods:</b> The complete sequences of the viroporins M2 (P06821), E (P59637) and SH (Q9DHE5) in FASTA format were entered and processed in the BepiPred-2.0 server (http://www.cbs.dtu.dk/services/BepiPred/) using the default 0.5 epitope threshold. The predicted epitopes with length&gt;5 residues were submitted in the MimoSearch and MimoBlast tools of the Biopanning Data Bank (http://immunet.cn/bdb/index.php) and were inquired for identical and similar mimotopes respectively. <b>Results:</b> Three sequential B-Cell epitopes were predicted in the M2 sequence (TEVETPIRNEW, SSD, KYGLKGGPSTEGVPKSMREEYRKEQQSAVDADDGHFVS) and two in the E and SH proteins (VSEET, YVYSRVKNLNSSEGVP and SKFW, EHKTFCNKTLEQGQMYQ respectively). No identical mimotopes were identified for the three proteins. The MimoBlast analysis identified two peptides, similar to the M2 epitopes. <b>Conclusions:</b> We have predicted sequential B cells epitopes from the M2, E and SH viroporins which should be further studied experimentally as their determination is important for the design of effective antiviral drugs.