1st International and 10th National Iranian Conference on Bioinformatics

Theoretical study of the inhibitory effect of bee venom peptides on coronavirus spike protein

Paper ID : 1034-ICB10

Authors:

مهتاب زارعان¹, کریم مهنام *²

¹گروه زیست شناسی، دانشکده علوم، دانشگاه شهرکرد، شهرکرد، ایران

²گروه زیست شناسی، دانشکده علوم، دانشگاه شهرکرد، شهرکرد

Abstract:

The spike protein of coronavirus binds to the ACE2 receptor protein at the surface of human cells and causes the entrance virus to the cell [1]. Bee venom peptides have anti-inflammatory effects and have been suggested for the treatment of coronary heart disease [2]. To test their ability for binding to the spike protein, the three-dimensional structure of the spike protein and peptides were downloaded from the protein bank or prepared by the Hypercom software and subjected to molecular dynamics simulation for 100 nanoseconds by the Gromacs software. The peptides were then docked to the RBD domain of the spike protein by the Haddock server and the complexes were simulated again for 100 ns. The binding energy of the peptides to the RBD domain was calculated by MM/PBSA method. The results showed that the peptides MISMLRCIYLFLSVILITSY and MKFLVNVALVFMVVYISFIY had better binding energy and could inhibit it better by binding to the spike protein and preventing the virus from entering the cells. Also, several mutations in these peptides were designed with the help of Beatmusic server, and the same procedure was repeated for them. The results showed that the MISMLRCIYLFLSVILITSY mutation had better binding energy than the others and this peptide suggests as a potential drug for coronavirus disease

Keywords:

Coronavirus, Spike protein, Molecular dynamics simulation, Bee venom peptides, Mutation

Status : Paper Accepted (Poster Presentation)