Journal of Advanced Chemical Engineering

Abstract

The Molecular Docking Study of Interaction of Newly Synthesised Benzamide Appended by Pyrazolone Derivatives as Ligand Molecule with the Target Protein 6LU7 of Novel Corona Virus

Pavithra V* and Sudha BS

Plants and bioactive compounds have played an important role in the development of several clinically useful therapeutic agents since time immemorial. The global health emergency of novel COVID-19 is due to severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). As if now there are no approved drugs for the treatment of corona viral disease (COVID-19), although some of the drugs have been tried. The virtual interaction of the COVID-19 main protease in complex with the inhibitor N³ (Research Collaborators for Structural Bioinformatics Protein Data Bank (PDB) ID: 6LU7), Hence this is chosen as target protein molecule. The newly synthesised compounds of benzamide appended pyrazolones derivatives are made as ligand molecules. The synthesis of these organic ligand molecules is done through four steps using different reagents and different environmental conditions. In this article we have discussed the interaction of our synthesized ligands with the target protein molecule using autodock tools. Firstly, the ligands were prepared using commercial ACD/chemsketch tool in PDB format. Desired protein target 6LU7 is downloaded from Protein Data Bank. Further protein optimization done by removing co-ordinates and hetero atoms, energy minimization of protein is done by Swiss PDB viewer 4.1.0. To change the file format open babel 2.4.1 is used. Docking of protein and ligand is done using autodock 4.2 and the results are visualized by pymol and tabulated using the Lamarckian genetic algorithm. After docking comparative study of the binding energies, inhibitory constant and hydrogen bonding of all interactions were discussed and tabulated for the good results.

Published Date: 2023-08-07; Received Date: 2023-07-04