Fusion protein targeted antiviral peptides: fragment based drug design (FBDD) guided rational design of dipeptides against SARS-CoV-2.

Infectious diseases caused by viruses become a serious public health issue in the recent past, including current pandemic situation of COVID-19. Enveloped viruses are most commonly known to cause emerging and recurring infectious diseases. Viral and cell membrane fusion is the major key event in case of enveloped viruses that required for their entry into the cell. Viral fusion proteins are playing important role in fusion process and in infection establishment. Because of this, fusion process targeting antivirals become an interest to fight against viral diseases caused by enveloped virus. Lower respiratory tract infections casing viruses like influenza, respiratory syncytial virus (RSV) and severe acute respiratory syndrome corona virus (SARS-CoV) are examples of such enveloped viruses that are at top in public health issues. Here, we summarized the viral fusion protein targeted antiviral peptides along with their mechanism and specific design to combat viral fusion process. The pandemic COVID-19, severe respiratory syndrome disease is outbreak worldwide. There are no definitive drugs yet but few are in on-going trial. Here, an approach of fragment based drug design (FBDD) methodology was used to identify the broad spectrum agent target to the conserved region of fusion protein of SARS CoV-2. Three dipeptides (DL, LQ and ID) were chosen from the library and designed by the systematic combination along with their possible modifications of amino acids to the target sites. Designed peptides were docked with targeted fusion protein after energy minimization. Results show strong and significant binding affinity (DL = -60.1 kcal/mol; LQ = -62.8 kcal/mol; ID= -71.5 kcal/mol) during interaction. Any one of the active peptides from the developed libraries may help to block competitively the target sites to successfully control COVID-19.