Computational drug design of novel COVID-19 inhibitor

Abstract

The numerical results of this study are presented in the tables presented below. This has become necessary because of the need to correlate some of the data. Other results, such as plots and pictorial representation of the interactions between the ligands and their receptor binding sites are presented as figures.

Table S2 shows the molecular docking result of the reference inhibitor and 1000 HIV 1 antiviral compounds on SARS-CoV-2 main protease receptor (PDB ID: 6XBH). The following parameters are shown: number of rotatable torsions, hydrogen bond energy, hydrophobic energy in exposing a surface to water, the van der Waals interaction energy (sum of gc and gh van der Waals), internal conformational energy of the ligand, the desolvation of exposed H-bond donors and acceptors, the solvation electrostatics energy change upon binding and mean force score. According to the molecular docking results, it was found that the binding energy of co-crystallized ligand, (R)-3-(((2R,5S)-5-(((S)-(benzyloxy)(hydroxy)methyl)amino)-1-hydroxy-4-oxo-6-phenylhexan-2-yl) amino)-1,3-dihydro-2H-pyrrol-2-one was − 23.56kCal/mol while the binding energy of all the 1000 HIV 1 antiviral inhibitors lies between − 4.73 and − 48.38 kCal/mol. Figure 1 is the docked poses of SARS CoV-2 main protease (PDB ID: 6XBH) with REF-IN (stick figure) while Table 3 shows the interaction types with surrounding amino acids of SARS CoV 2 Main Protease (PDB ID: 6XBH) with REF-IN.