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.