Lectron microscopy structure of the SARS-CoV-2 RNA-dependent RNA polymerase (Protein Information Bank [PDB] ID: 6M71) was obtained from the Analysis Collaboratory for Structural Bioinformatics (RCSB) Protein Information Bank. The structure of all ligands (Ellipticine, Ecteinascidin, Homoharringtonine, Dolastatin ten, Halichondrin, and Plicamycin) was also downloaded in the PubChem database and saved within the.sdf format. These S1PR4 supplier structures from the.sdf file had been subsequently converted to the.pdb format utilizing the OpenBabel software, that is cost-free computer software that presents a remedy for conversion between numerous chemical file formats [42].Fig. 1. Three-dimensional (3D) structure and putative binding site: (a) 3D ribbon structure of your SARS-CoV-2 RdRp protein (receptor), (b) 3D structure of PKD1 Molecular Weight Ellipticine (ligand), (c) putative binding web site of Ellipticine around the SARS-CoV-2 RdRp protein (Ellipticine interaction with SARS-CoV-2 RdRp), (d) 3D structure of Plicamycin (ligand), (e) putative binding web page of Plicamycin on the SARS-CoV-2 RdRp protein (Plicamycin interaction with SARS-CoV-2 RdRp), (f) 3D structure of Dolastatin, and (g) putative binding internet site of Dolastatin around the SARS-CoV-2 RdRp protein (Dolastatin interaction with SARS-CoV-2 RdRp).R. Bharti, S.K. ShuklaJournal of Electronic Science and Technology 19 (2021)2.two. Molecular docking PatchDock, on the internet docking software, was applied to dock the ligands with the SARS-CoV-2 RNA-dependent RNA polymerase protein. It was also used to carry out structure prediction for protein-small molecule complexes. Furthermore, it truly is a geometry-based molecular docking algorithm and also the servers of this software program are extremely efficient, the key cause behind which can be its speedy transformational search driven by nearby function matching [40]. The.pdb structures of each ligand as well because the protein were submitted around the on the net portal of PatchDock, which provided the docked lead to a few minutes. The structure with all the prime score was downloaded and analyzed. PyMOL was used to visualize the resultant docked structures; it is a user-sponsored molecular visualization program often utilized for molecular visualization by crystallographic and molecular dynamics simulation. All of the docked structures were offered in figures [43]. two.three. Prediction of Lipinski’s rule of 5 properties Lipinski’s rule of five is actually a rule of thumb that assists with distinguishing amongst drug-like and non-drug molecules. Lipinski’s rule of five contains the following guidelines: i) Molecular mass need to be significantly less than 500 Da (Da), ii) higher lipophilicity, iii) significantly less than 5 hydrogen bondFig. two. 3D structure and putative binding web site: (a) 3D ribbon structure of the SARS-CoV-2 RdRp protein (receptor), (b) 3D structure of Ecteinascidin, (c) putative binding web-site of Ecteinascidin around the SARS-CoV-2 RdRp protein (Ecteinascidin interaction with SARS-CoV-2 RdRp), (d) 3D structure of Halichondrin, (e) putative binding website of Halichondrin around the SARS-CoV-2 RdRp protein (Halichondrin interaction with SARS-CoV-2 RdRp), (f) 3D structure of Homoharringtonine, (f) putative binding web page of Homoharringtonine on the SARS-CoV-2 RdRp protein (Homoharringtonine interaction with SARS-CoV-2 RdRp).R. Bharti, S.K. ShuklaJournal of Electronic Science and Technology 19 (2021)donors, iv) significantly less than 10 hydrogen bond acceptors, and v) molar refractivity must be among 40 and 130. Drug likeness is seen when a molecule complies with two or much more of these guidelines, helping with screening for tested ligands with drug-like pro.