Original Article

Molecular Docking Study of Several Seconder Metabolites from Medicinal Plants as Potential Inhibitor of COVID-19 Main Protease


  • Sinan Bilginer
  • Sefa Gozcu
  • Zuhal Guvenalp

Received Date: 06.08.2021 Accepted Date: 24.09.2021 Turk J Pharm Sci 0;0(0):0-0 [e-Pub]


Coronaviruses (CoVs) are known to cause infections that affect the respiratory tract, liver, central nervous and the digestive systems in humans and animals. This study focused on the main protease (Mpro) in CoVs (PDB ID: 6LU7) that is used as a potential drug target to combat 2019-CoV. In the present study, total of 35 secondary metabolites from medical plants were selected and docked into the active site of 6LU7 by molecular docking studies to find out a potential inhibitory compound that may be used to inhibit the COVID-19 infection pathway.

Materials and Methods:

The chemical structures of the ligands were obtained from the Drug Bank (https://www.drugbank.ca/). AutoDockTools (ADT ver.1.5.6) was used for molecular docking studies. The docking results was evaluated by using BIOVIA Dıscovery Studio Visualizer and and PyMOL (ver. 2.3.3, Schrodinger, LLC).


Pycnamine, tetracannabinol, oleuropein, quercetin, primulic acid, kaempferol, dicannabidiol, lobelin, colchicine, piperidine, medicagenic acid, and narcotine are found to be potential inhibitors of the COVID-19 Mpro. Among these compounds, pycnamine which was evaluated against COVID-19 for the first time showed high affinity to the COVID-19 Mpro compared with other seconder metabolites and reference drugs.


Our results obtained from docking studies suggest that pycnamine should be examined in vitro to combat 2019-CoV. Moreover, pycnamine might be a promising lead compound for anti-CoV drugs.

Keywords: COVID-19, molecolar docking, pycnamine, seconder metabolties.