With the spread of the coronavirus in all countries of the world and in the absence of a vaccine or effective treatment to inhibit the infection. Several medicinal plants are used by the Moroccan population either to treat or prevent infection. The frequent use of its plants without documentation of their effectiveness on the Covid-19 is justified by cultural and economic reasons and their pharmacological activity scientifically proven. The objective of this study is to evaluate the inhibitory effect of the main polyphenols and flavonoids of Syzygium aromaticum and citrus limon as well as the main organosulfur compounds of garlic against coronavirus 6lu7 protease and 6y2e protease using in-silico molecular docking analysis.
The COVID-19 3CLpro/Mpro (PDB ID: 6LU7) and free enzyme of the SARS-CoV-2 (2019- nCoV) main protease (PBD ID: 6Y2E) structures were obtained from the https://www.rcsb.org/ website in .PDB format. The COVID-19 3CLpro/Mpro (PDB ID: 6LU7) and main protease (PBD ID: 6Y2E) were prepared using autodock tools from MGL Tools package http://mgltools.scripps.edu/.
The reactive molecular dynamics simulations were performed using the software LAMMPS and the ReaxFF force field. In this force field, the general energy function
We have docked 34 natural products belonging to the three medicinal plants. In 6LU7 protease, 24 compounds exhibited a binding affinity greater than or equal to -6 Kcal/mol. While, in 6Y2E protease, 6 compounds exhibited a binding affinity greater than or equal to -6 Kcal/mol.
We found that ellagic acid, narirutin, neoeriocitrin and neohesperidin are highly suggested as an inhibitor of SARS-COV-2.