Lasioglossin-1 peptide inhibits binding of spike protein of SARS-CoV-2 to ACE2 receptor: an in silico approach of some bee venom peptides

ABSTRACT

The coronavirus prevalent, initiated by the SARS-CoV-2 virus, has induced a global health crisis, recently. Coronavirus can bind to ACE2 receptors on the surface of human cells and infect them through the RBD domain of spike protein. Bee venom peptides have anti-inflammatory effects and were proposed for coronavirus cure. To investigate this proposal, 11 peptides from bee venom were selected and 3D structures of them were prepared. Each peptide was simulated for 100 ns molecular dynamics simulation and 22 conformations were extracted from the last 20 ns of MD simulation. Then All 220 conformations were docked to the RBD domain of spike protein by haddock server and the best complexes for each peptide were chosen for another 100 ns MD simulation. Then MM/PBSA binding free energy calculations were done. The results revealed that the Lasioglossin-1 peptide (VNWKKVLGKIIKVAK) had better interaction with the RBD domain of spike protein than other peptides and can reduce virus entrance to human cells. This peptide can be a potential drug for coronavirus. Also, to find a probable better peptide, two mutations were created in this peptide, and previous procedures were repeated and it determined that none of the mutated peptides were better than native Lasioglossin-1.

KEYWORDS:

• Spike protein of Coronavirus
• molecular dynamics simulation
• Bee venom peptides
• peptide docking
• MM/PBSA binding free energy

Acknowledgment

The authors thank the Shahrekord University of Iran for funding this project.

Disclosure statement

No potential conflict of interest was reported by the author(s).