Evaluation of SARS-CoV-2 inhibition of some compounds inCYMBOPOGON CITRATUS oil combining docking and molecular dynamics simulations

Abstract

The visual screening and simulation methods were used to evaluate the inhibitory ability of 34 compounds in Cymbopogon citratus oil against SARS-CoV-2. We chose the best compound, SC22, with a DS of -12.80 Kcal. mol-1 with a distance RMSD of 0.23. This was the most effective compound at inhibiting the viral protein 6LU7. For the protein ACE2 or an endemic host receptor, the docking ability of SC22 showed DS = -13.13 Kcal.mol-1 and RMSD = 1.32 Å; SC10 docked in DS = -12.79 Kcal.mol-1 and RMSD = 0.91 Å; SC11 gave the docking values DS = -12.77 Kcal.mol-1 and RMSD = 1.15 Å. SC26 showed DS = -12.76 Kcal.mol-1 and RMSD = 1.44 Å; SC20 showed DS = -12.68 Kcal.mol-1 and RMSD = 1.22 Å; the Cymbopogon citratus oil involved the potential compounds for contributing to drug development. The compounds SC10, SC11, SC20, SC22 also tested and refined the druglikeness properties. The compound SC22 gives many druglikeness properties and is easy to carry out drug synthesis.