Computational Study on SARS-CoV-2 Viral Protein Interaction with Natural Compounds of Coriandrum sativum L

ABSTRACT

The SARS-COV-2 become a global pandemic causing significant mortality and morbidity all around the world. Until now there are no effective drugs or vaccines available against SARS-CoV-2. In this regard, medicinal plants captured enormous attention, as natural products are safe and easily available bioactive compounds in which maintain the disease homeostasis. Amongst, natural compounds of Coriandrum sativum L (coriander) have proved to be effective in viral infection, as they possess antiviral and anti-inflammatory activities. However, molecular regulation of such bioactivities remains elusive. We performed molecular docking analyses using AutoDock Vina to investigate the potential inhibitory activities of the seven natural compounds of coriander (limonene, geraniol, gamma-terpinene, geranyl acetate, caffeic acid, ferulic acid, gallic acid) against the essential proteins of SARS-CoV-2 (main protease (Mpro), nonstructural protein-13 (NSP-13), Papaine like protease (PLpro) and RNA dependent RNA polymerase(RdRp)) together with two main inflammatory proteins ( cyclooxygenase-2 (COX-2) and interleukin-6 (IL- 6)). The empirical and knowledge-based algorithm of AutoDock Vina was utilized to calculate free binding energies of ligands and BIOVIA discovery studio 2020 tool was used to visualize docking results. Our results reveal that gallic acid has a strong binding affinity to Mpro (-5.8 kcal/mol) and NSP13 (-7.0 kcal/mol) forming five and three conventional hydrogen bonds respectively. Further, caffeic acid demonstrates a higher binding affinity to PLpro (-7.4 kcal/mol) and RdRp (-6.7 kcal/mol) while securing four and three conventional hydrogen bonds respectively. Interestingly, both COX-2 (-6.9 kcal/mol) and IL-6 (-6.3 kcal/mol) also show a higher binding affinity to gallic acids. In addition, gallic acid stabilizes three conventional hydrogen bonds with COX-2 whereas it forms four conventional hydrogen bonds with IL-6. Further, drug-likeness properties of gallic acid and caffeic acid were determined using the SWISSADME server. Our results show that both gallic acid and caffeic do not violate Lipinski rules suggesting these compounds as new antiviral and anti-inflammatory drug candidates for SARS-CoV-2. © 2022 IEEE.