Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2

Jaka Fajar Fatriansyah; Raihan Kenji Rizqillah; Muhamad Yusup Yandi; Fadilah; Muhamad Sahlan

doi:10.1016/j.jksus.2021.101707

Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2

J King Saud Univ Sci. 2022 Jan;34(1):101707. doi: 10.1016/j.jksus.2021.101707. Epub 2021 Nov 15.

Authors

Jaka Fajar Fatriansyah¹, Raihan Kenji Rizqillah¹, Muhamad Yusup Yandi¹, Fadilah², Muhamad Sahlan³

Affiliations

¹ Department of Metallurgical and Materials Engineering, Faculty of Engineering, Universitas Indonesia, Kampus Depok, Jawa Barat 16424, Indonesia.
² Department of Medicinal Chemistry, Faculty of Medicine, Universitas Indonesia, Salemba Raya, Jakarta 10430, Indonesia.
³ Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Kampus Depok, Jawa Barat 16424, Indonesia.

Abstract

Molecular docking and dynamics simulations were conducted to investigate the antiviral activity of Propolis Sulabiroin-A to inhibit the SARS-CoV-2 virus with quercetin, hesperidin, and remdesivir as control ligands. The parameters calculated were docking score and binding energy/molecular mechanics-generalized born surface area (MMGBSA), root mean square displacement (RMSD), and root mean square fluctuation (RMSF). Docking and MMGBSA scores showed that all the ligands demonstrate an excellent candidate as an inhibitor, and the order of both scores is hesperidin, remdesivir, quercetin, and sulabiroin-A. The molecular dynamics simulation showed that all the ligands are good candidates as inhibitors. Although the fluctuation of Sulabiroin-A is relatively high, it has less protein-ligand interaction time than other ligands. Overall, there is still a good possibility that sulabiroin-A can be used as an alternative inhibitor if a new structure of receptor SARS-CoV-2 is used.

Keywords: COVID-19, Corona Virus Disease 2019; Drug discovery; MD, Molecular Dynamic; MM-GBSA, Molecular Mechanics/Generalized Born Surface Area; Molecular docking; Molecular dynamics; RMSD, Root Mean Square Deviation; RMSF, Root Mean Square Fluctuation; SARS-CoV-2; SARS-Cov-2, Severe acute respiratory syndrome coronavirus 2; Sulabiroin-A.