Searching Potential Molecules Against SARS-CoV-2 from Costus arabicus L. Root Smoke: A Docking Study

Abstract

Background: The root smoke of Costus arabicus L. (Qust-e Shirin) has been used in Iranian traditional medicine (ITM) for rhinorrhea and catarrh, especially with infectious origin. Objectives: This study aimed to inspect potential anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activities of chemical compositions of this smoke through a docking study. Materials and Methods: Based on our previous study on the chemical compositions of C. arabicus root smoke, the chemical structure of components was revealed by GC-MS. In this study, these structures were generated in HyperChem software, and an energy-minimization procedure was performed for the molecules. For the docking study, the Hex software was used. Docking was performed using the Protein Data Bank (PDB) structure of the COVID-19 RNA-dependent RNA polymerase (RdRp) (PDB ID: 6M71) enzyme which was obtained from PDB bank, water molecules were removed, Coleman charge was added, and non-polar hydrogens were merged. Then, docking was performed. Results: The result indicated the energy of each interaction between molecules and enzymes. The lower the energy, the higher the probability of interaction will be. The best molecule was 6H-quindoline which has the best total energy among the molecules. The next molecule was 5-methoxy-alpha methyl tryptamine with -210.82 kcal energy. Their similar structure in indole moiety suggests that this fragment can play a crucial role in attachment to the enzyme and can be kept intact in future designs against COVID-19 inhibitors. Conclusion: In conclusion, this study showed that C. arabicus root smoke may be effective in SARS-CoV-2 infection. Further in vitro and in vivo studies on the activity of the smoke and its constituents against COVID-19 would be fruitful.