Computational evaluation of Artemisia annua compounds for antiviral activity against SARS-CoV-2 and hepatitis B virus using molecular docking, MM-GBSA, and molecular dynamics simulation

Abstract

Artemisia annua, a well-known medicinal plant is used in different parts of the world for various purposes. In this study, in silico approaches have been considered to evaluate the antiviral potential of A.annua-derived compounds against COVID-19 and Hepatitis B receptors. The Mpro and the Rdrp were used as receptors for COVID-19, and DDB1-HBx and HBCAG for viral Hepatitis B. The molecular docking, rutin (− 8.97 ± 0.04 kcal/mol against Mpro and − 8.67 ± 0.13 kcal/mol against Rdrp), astragalin (− 8.50 ± 0.17 kcal/mol against Mpro and − 9.5 ± 0.2 kcal/mol against DDB1), Isoquercetin, quercimeritrin, and cynaroside were the five lead hits against COVID-19 and the Hepatitis B virus. The stability comparison between 2 complexes (Mpro-Rutin and Mpro-Astragalin) after molecular dynamics simulations (MDS) performed at 100 ns has shown that the first complex is more stable than the second. This observation is confirmed after MMGBSA is performed. The complex between Mpro-Rutin exhibits a superior binding affinity while Mpro-Rutin is weaker. The complex between HBCAG-Rutin is slightly stable compared to HBCAG-Cynaroside after MDS, while after MMGBSA, their binding energies are similar. The remaining parameters of MDS, such as rGyr, MolSA, SASA, and PSA, were within the recommended range.