Investigating the antiviral effect of CLF36 and CLFarm peptide on P32 protein of sheeppox virus through molecular docking simulation

Sheeppox is one of the most common diseases in sheep that can spread quickly in the herd. Currently, there is no specific treatment for this viral disease. The purpose of this study was to investigate the antimicrobial peptide CLF36 and CLFarm on the surface protein of the sheep pox virus P32 protein and the cellular receptors of this protein such as heparin sulfate and UDP-N-acetyl glucosamine. The third structure of P32 was done using software such as I-TASSER. The interactions were performed statically in a computer by bioinformatics tools such as HDOCK software and using Gromacs in the molecular dynamics section. The results of this study showed that the amino acids of CLF36 peptide involved in hydrogen bonding with P32 include D1, K5, V8, Q11, K9, R16, R22, K25, R27 and K34 and for CLFarm include K5, K9, Q11, K13, R27, W30, Q31 and K35. Docking results showed that peptides were attached to three epitope regions EP1,4,8 in P32 protein. In connection with the molecular docking between CLF36 arm and the two receptors UDP-N-acetylglucosamine and heparin sulfate, the hydrogen bonds included Gln 11, Trp 30 and Trp 4, Trp 30, Gln 11, Arg 27, Cys 33, respectively; Although CLF36 had weak binding energy with these two receptors. In the molecular dynamics section, the graph of RMSF and RMSD and Gyrate showed a few fluctuations, which were ignored. Finally, these results showed that both peptides have a good performance against P32 in a period of 50 ns.