Inhibition of the Ras/Raf/extracellular signal‑regulated kinase 1/2 signaling pathway by compounds of natural origin for possible treatment of spinal cord injury: An in silico approach

Spinal cord injury (SCI) is a severe disease associated with permanent neurological deficit. Recent studies in the treatment of SCI have demonstrated that the Ras/Raf/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway serves an important role in the disease etiology, and that upregulation of this signaling pathway is associated with the development of SCI. In the present study, inhibition of Ras protein was employed in order to downregulate the Ras/Raf/ERK1/2 signaling pathway using compounds of natural origin from the Interbioscreen natural compound database. To the best of our knowledge, this is the first study using a chemical-computational approach in order to identify novel small molecule inhibitors for Ras. A database of ~50,000 compounds was selected for virtual screening, setting a free energy binding bias of -7 kcal/mol to limit the number of compounds. The subset of compounds generated by virtual screening was further limited by subjecting these to the Lipinski's rule of five parameters. A total of five shortlisted compounds were subjected to molecular docking simulation. The compounds were docked into the GTP binding site of Ras, and the inhibition of this site was examined as a promising strategy for the downregulation of Ras/Raf/ERK1/2 signaling pathway. The compounds bound to the GTP binding site through hydrogen bonds and hydrophobic interactions. The identified lead compound was then subjected to molecular dynamics simulation, and the results revealed that GLY60 in the GTP binding site of Ras protein was the optimal binding site during a 100 nsec run.