Molecular dynamics simulation study on the drug discovery in covid-19 disease

Subject Areas :

Pejman Shir Ali Poor ¹ , Elham Tazikeh-Lemeski ²

1 - Department of Chemistry, Gorgan Branch, Islamic Azad University, Gorgan, Iran
2 - Department of Chemistry, Gorgan Branch, Islamic Azad University, Gorgan, Iran

Received: 2022-03-05 Accepted : 2022-03-05 Published : 2021-03-01

Keywords: Molecular dynamics simulations, Coronavirus (COVID-19), SARS-CoV-2 nsp-16, Kumusine,

Abstract :

In this study, drug discovery of SARS-CoV-2 nsp-16 effective in Coronavirus (COVID-19) has been accomplished by pharmacophore-based virtual screening among some analogs (FDA approved drugs) and marine natural plants (MNP). The comparison of the binding energies and the inhibition constants was determined using molecular docking method. Between selected drugs, three compound were selected for further investigation using the molecular dynamics simulations. The results indicated that Ibrutinib and Idelalisib are oral medications while Kumusine, with proper hydrophilic and solubility properties, is an appropriate candidate for nsp-16 inhibitor and can be effective to control COVID-19 disease. It seems that Kumusine due to its better drug properties including the highest binding, the ability of destroying the secondary structure of the protein can be proposed as the best drug candidate among screened drugs in this research, for further investigations.