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Dr. Muhammad Baqir MR Fakhrildin
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Abstract

MOLECULAR DOCKING AND MOLECULAR DYNAMIC SIMULATIONS FOR NATURAL ANTIVIRAL COMPOUNDS AGAINST SARS-COV-2: COMPUTATIONAL INVESTIGATION

Desai S. A.* and Meshram D. B.

ABSTRACT

A new coronavirus was identified as the COVID-19 virus; it is the etiological agent responsible for the 2019-2020 viral pneumonia outbreak. The infection began in Wuhan, China At the end of December 2020. Currently, there is no antiviral drug available to control the infection, and options in medical treatments are limited. We have used a computer-aided drug design approach to find active compounds against the virus. We have identified a total of seventyeight natural compounds with antiviral properties. The PubChem database is used to retrieve the structures in 2D format. We have used the main protease named 5REH as a target. We have used PyRx to dock using a standard protocol. We have further investigated compounds with good binding affinity for their ADMET profile using computational approaches. This study leads us to have three compounds named Lycorine, Corylifol, and Broussochalcone. Molecular dynamic simulation studies were done to check the stability of the protein and ligand complex during a simulation. Parameters like RMSD, RMSF, and radius of gyration were observed to understand the fluctuations. We also have performed the simulation for standard ligand AWP to compare the stability with test ligands. All the results obtained were showing deviations from the standard values but all the deviations were not statistically significant. Protein-ligand interaction studies also reveal that enough hydrogen and hydrophobic bonds are present to justify our results. The three compounds namely lycorine, Corylifol, and Broussochalcone A identified can come out as a potential candidate for the treatment of Covid -19 infections.

Keywords: Molecular Docking, MD simulation, Covid-19, Protease, VMD and NAMD, RMSD.


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