Prediction of proteins associated with covid-19 based ligand designing and molecular modeling

Abstract

Current understanding about how the virus that causes COVID-19 spreads is largely based on what is known about similar coronaviruses. Some of the Natural products are suitable drugs against SARS-CoV-2 main protease. For recognizing a strong inhibitor, we have accomplished docking studies on the major virus protease with 4 natural product species as anti COVID-19 (SARS-CoV-2), namely “Vidarabine”, “Cytarabine”, “Gemcitabine” and “Matrine” which have been extracted from Gillan's leaves plants. These are known as Chuchaq, Trshvash, Cote-Couto and Khlvash in Iran. Among these four studied compounds, Cytarabine appears as a suitable compound with high effectiveness inhibitors to this protease. Finally by this work we present a method on the Computational Prediction of Protein Structure Associated with COVID-19 Based Ligand Design and Molecular Modeling. By this investigation, auto dock software (iGEM-DOCK) has been used and via this tool, the suitable receptors can be distinguished in whole COVID-19 component structures for forming a complex. “iGEMDOCK” is suitable to define the binding site quickly. With docking simulation and NMR investigation, we have demonstrated these compounds exhibit a suitable binding energy around 9 Kcal/mol with various ligand proteins modes in the binding to COVID-19 viruses. However, these data need further evaluation for repurposing these drugs against COVID-19 viruses, in both vivo & vitro.