The comparison of binding affinity of Black seed and Licorice compounds with Remdesivir to Mpro of Sars-CoV-2 using steered molecular dynamics simulation

SARS-CoV-2 which caused to Covid-19 was reported as an epidemic by the World Health Organization (WHO). In this virus, one of the essential cysteine proteases, which is called the main protease, can be used as a drug target for many herbal and chemical inhibitors. One of the factors in the effectiveness of drugs inhibitory is the binding affinity of them to main protease. In this paper, the comparison of the binding affinity of herbal compounds (Nigelidine, from black seed and Liquiritigenin from licorice plant) with Remdesivir on the main protease from SARS-CoV-2 has been investigated using steered molecular dynamics simulation. The results showed that Nigelidine has the highest rupture force among herbal ligands. Despite of the fact that Remdesivir has the highest rupture force compared to herbal inhibitors. Also, the electrostatic and van der Waals energy for Remdesivir and main protease shows a more negative value than other herbal inhibitors. Therefore, despite of the high dock score of the compounds of black seed and licorice, Remdesivir as a chemical compound shows more binding affinity.