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

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 angstrom;SC10 docked in DS = -12.79 Kcal.mo1(-1) and RMSD = 0.91 angstrom;SC11 gave the docking values DS = -12.77 Kcal.moL(-1) and RMSD = 1.15 angstrom. SC26 showed DS = -12.76 Kcal.moL(-1) and RMSD = 1.44 angstrom;SC20 showed DS = -12.68 Kcal.moL(-1) and RMSD = 1.22 angstrom;the Cymbopogon cifratus 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.

Study on SARS-CoV-2 inhibition of some potential drugs using molecular docking simulation

Inhibitory capabilities of six old drugs selected from the DrugBank database including Losartan, Triazavirin, TMC-310911, Verapamil, Clevudine and Elbasvir, which are promising for the treatment of an infectious disease caused by SARS-CoV-2, were examined on the host receptor Angiotensin-converting enzyme 2 (ACE2) and the main protease (PDB6LU7) of SARS-CoV-2 using molecular docking simulation. Results reveal that both proteins ACE2 and PDB6LU7 are in strong inhibition by the drugs and the inhibitory effectiveness is in the order: Clevudine > Triazavirin > TMC-310911 > Elbasvir > Losartan > Verapamil. In particular, the inhibitability highly correlates with the average docking score energy of inhibitory complexes, and drug-protein active interactions. Regarding inhibitory ligands, their polarizability, molecular size, and dispersion coefficient logP are also significant indicators for inhibition potential. The drugs are suggested as valuable resources for selecting potential pharmaceuticals to prevent SARS-CoV-2 invasion into human body given theoretical demonstration of molecular docking simulation. © 2020 Vietnam Academy of Science and Technology, Hanoi & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim