Comparative study on quantum descriptors, molecular docking and dynamic simulation of antiviral drugs with Covid-19

Abstract

Covid-19 is a beta-coronavirus that was first identified during the Wuhan COVID-19 epidemic in 2019. This study is focused on the quantum descriptors of the proposed antiviral drugs, molecular docking, and dynamics simulation with the main protease of coronavirus. Such drugs are Baloxavir, Chloroquine, Avigan, Plaquenil, oseltamivir, Remdesivir, Arbidol, and Sofosbuvir were used for comparison. Density functional theory (DFT) may help find the relevancy of quantum chemical descriptors to explain the potential antiviral activity, Some quantum descriptors such as ΔE; the energy gap, η; global hardness, S; global softness, I: ionization potential, A: electron affinity, χ: absolute electronegativity, ω; ΔE Back-donation; the back donation were calculated based on EHOMO; energy of the highest occupied molecular orbital, and ELUMO; energy of the lowest unoccupied molecular orbital. Fukui indices (f+, f−); for local nucleophilic and electrophilic attacks are investigated for the investigated antiviral drugs. The reported genomic sequence of Covid-19 main protease in complex with an inhibitor N3 (DOI: https://doi.org//10.2210/pdb6LU7/pdb) was used as a precursor for docking with the selected drugs after removing the attached inhibitors N3 and water. Molecular docking was performed using Autodock 4.2, with the Lamarckian Genetic Algorithm, and was analyzed by Autodock 1.5.6 and Pymol version 1.7.4.5 Edu, However, further research is necessary to investigate their potential medicinal use.