Figure 13: The best positions of the Chloroquine in the proteins 6M03, 5R7Y, 6W63, 5R81 and 5R84.
Results reveal that the interactions are mainly of two types: Van der Walls and hydrogen-bonding. The VDW energies interactions are stronger than H-bonding interactions, and all the compounds not have shown electronic interactions. Fig. S3 presents several forms of intermolecular interactions between ligand and protein. Acceptor-donor electronic interactions allow the construction of hydrogen-bonding interactions. The docked ligand interactions with amino acids constituting the active site of the receptor are showed in fig. 13 and table 8. Total energy scores are at a very comparable level with an average energy of -73.274 kcal/mol. Among these series of complexes, the Chloroquine-6M03 displayed better inhibition when compared with others, since it was found to be the strongest binding energy (-81.866 kcal/mol). It had formed two H-bond interactions with LEU-141 and SER-144. The H-bond interaction was found to be -6.285 kcal/mol (fig. S3). Additionally, the van der Waals interactions (E=-75.581 kcal/mol) were also being formed with HIS-41, LEU-141, ASN-142, ASN-142, MET-165, GLU-166 and GLU-166 residues. Also, Chloroquine has a good binding interaction with 5R7Y protein and it exhibited the total energy score of -77.498 kcal/mol. The docking pose analysis of this complex revealed that the Chloroquine is oriented with the VDW interactions surrounded by the chains of LEU-141, ASN-142, ASN-142, MET-165, GLU-166 and GLU-166 in the 5R7Y protein (-70.605 kcal/mol). As seen from the Table 8, there are seven conventional VDW interactions between the 6W63 and the Chloroquine molecule (-70.961 kcal/mol) and only a hydrogen bond interaction (-4.203 kcal/mol). For the enzyme of PDB ID: 5R81: THR-26 form one H-bond interaction; THR-26, THR-26, HIS-41, MET-49, ASN-142, ASN-142 and GLY-143 forms seven van der Waals interactions. Finally, amino acids HIS-41, ASN-142, ASN-142, MET-165, GLU-166 and GLU-166 forms VDW interactions for PDB ID: 5R84 (-63.327 kcal/mol). The total energy score of this complex was calculated and found to be -68.216 kcal mol-1. The molecular docking results suggest that the docked Chloroquine forms steady complexes with the different receptors which give minimum energy values. It reveals inhibition activity against 6M03, 5R7Y, 6W63, 5R81 and 5R84 enzymes. So, we can conclude that the Chloroquine can be considered as a potent inhibitor against COVID-19 virus.