3. RESULTS:
3.1 DOCKING:
The docking analysis of the compounds docked with Mpro and spike protein
of SARS-CoV-2 yielded negative values for free energy respectively they
were as follows. The grid box expressed negative values for free
energies observed in Mpro they are -1.068 KJ/mol was observed for
Eritadenine, -3.167 KJ/mol for Gallic acid, -0.420 KJ/mol for Ergosterol
peroxide and -5.035 KJ/mol for Pleuran. Similarly, the values of free
energies observed in Spike Protein were -0.783 KJ/mol, -2.140 KJ/mol,
1.027 KJ/mol and -5.241 KJ/mol respectively for the above four
compounds. The binding confirmations of the docked protein of Mpro are
hydrogen bonds and salt bridge formation for Eritadenine, hydrogen bonds
were formed in Gallic acid, hydrogen bond and hydrophobic interactions
were developed in Ergosterol peroxide and hydrogen bonds were formed
with the molecule of Pleuran. Correspondingly, the binding confirmations
of the docked protein of spike protein are hydrogen bonds were formed in
the ligands of eritadenine, gallic acid and pleuran; the hydrogen bonds
and hydrophobic interactions are developed in the compound Ergosterol
peroxide.
3.1.1 ERITADENINE:
3.1.1.1 DOCKED POSE AND PROTEIN LIGAND INTERACTION:
The docked pose of the ligand eritadenine along with protein ligand
interaction is given in the figures 2a, 2a1, 2b and 2b1. And protein
ligand interactions are tabulated in Table-1.
3.1.2 GALLIC ACID:
3.1.2.1 DOCKED POSE AND PROTEIN LIGAND INTERACTION:
The docked pose of the ligand gallic acid along with protein ligand
interaction is given in the figure 2c, 2c1, 2d and 2d1. And protein
ligand interactions are tabulated in Table-2.
3.1.3 ERGOSTEROL PEROXIDE:
3.1.3.1 DOCKED POSE AND PROTEIN LIGAND INTERACTION:
The docked pose of the ligand ergosterol peroxide along with protein
ligand interaction is given in the figure 2e, 2e1, 2f and 2f1. And
protein ligand interactions are tabulated in Table-3.
3.1.4 PLEURAN
3.1.4.1 DOCKED POSE AND PROTEIN LIGAND INTERACTION:
The docked pose of the ligand pleuran along with protein ligand
interaction is given in the figure 2g, 2g1, 2h and 2h1. And protein
ligand interactions are tabulated in Table-4.
3.2 MOLECULAR DYNAMICS:
3.2.1 ROOT MEAN SQUARE DEVIATION (RMSD) AND ROOT MEAN SQUARE FLUCTUATION
(RMSF):
The RMSD, RMSF produced from the docked compounds with targets Main
Protease (MPro) and Spike Protein (S) are given as Figure 3a, 3b, 4a and
4b as follows:
3.2.2 HYDROGEN BONDING:
The hydrogen bonding which was formed during the molecular dynamics
simulation was tabulated in Tables 5, 6, 7 and 8 for the ligand-protein
bound complexes of Main Protease (MPro) and in Tables 9, 10, 11, and 12
for the docked complexes of Spike Protein (S).
3.3 ADME PREDICTION:
3.3.1 ERITADENINE:
The results which appeared after the submission of Eritadenine molecule
in the SWISS-ADME database showed that the molecule, Eritadenine 18
heavy atoms, 7 hydrogen bond acceptors, 4 hydrogen bond donors and
147.38 Å2 of Topological Polar Surface Area (TPSA).
The lipophilicity parameters are optimal in nature. The estimated
solubility of Eritadenine is -0.36 which points it to be in the very
soluble class, in silico prediction of aqueous solubility with
response to TPSA is about -0.75 which categorizes to very soluble class
as well, water solubility by fragmental method puts the compound to very
soluble class with assigning the value of -0.29. The pharmacokinetics
properties determined that Eritadenine has low gastrointestinal
absorption, non-blood brain barrier permeant, does not act as P-gp
substrate and does not inhibit factors such as CYP1A2, CYP2C19, CYP2C9,
CYP2D6 and CYP3A4. The molecule is skin permeable with log Kp rate about
-9.14cm/s. And the molecule obeys Lipinski’s rule of five and Muegge
rules of druglikeness and also obeys Pan-Assay Interference Compounds
(PAINS), Brenk, Leadlikeness rules of medicinal chemistry.
3.3.2 GALLIC ACID:
The results of Gallic acid contains 12 heavy atoms, 5 hydrogen bond
acceptors, 4 hydrogen bond donors and TPSA is found to be 97.99
Å2. The lipophilicity parameters were very optimal for
the ligand. And water solubility parameters were soluble in nature as
predicted values are -1.64, -2.34 and -0.04 with respect to estimated
solubility (Log S-ESOL), in silico prediction of solubility with
reference to TPSA (Log S- Ali) and water solubility by fragmental method
(Log S- SILICOS-IT) which gives an inference of very soluble, soluble
and soluble classes according to the values projected. Estimated
pharmacokinetic data projects that the Gallic acid is highly absorbable
gastrointestinally, non- blood brain barrier permeant, non-P-gp
substrate, does not inhibit potential cytochrome P450 enzymes as
mentioned above, also has skin permeability rate of -6.84 cm/s. And the
compound obeys druglikeness rules such as Lipinski’s, Veber and Egan.
But the molecule doesn’t obey any rules of medicinal chemistry.
3.3.3 ERGOSTEROL PEROXIDE:
The ligand Ergosterol peroxide has 31 heavy atoms, 3 hydrogen bond
acceptors and 1 hydrogen bond donor and TPSA is about 38.69
Å2. They are highly lipophilic in nature. The water
solubility parameters are with predicted values of -6.46 for Log S- ESOL
which is poorly soluble, -7.33 for Log S-Ali which is poorly soluble and
-4.51 for Log S- SILICOS-IT which is moderately soluble. The
pharmacokinetic estimated data exclaims that the molecule is highly
absorbable gastrointestinally, non- blood brain barrier permeant,
non-P-gp substrate, does not inhibit potential cytochrome P450 enzymes
such as CYP1A2, CYP2C19, CYP2C9, CYP2D6 and CYP3A4. It also has skin
permeability rate of -4.15 cm/s. Ergosterol peroxide obeys druglikeness
rules of Lipinski and Veber. There’s no PAINS violation in medicinal
chemistry rules.
3.3.4 PLEURAN:
Pleuran has 41 hydrogen bond acceptors, 26 hydrogen bond donors and it
has TPSA about 664.43 Å2. They are highly lipophilic
and less hydrophilic in nature. The pharmacokinetic data shows that the
molecule is a non P-gp substrate, highly absorbable gastrointestinally,
non- blood brain barrier permeant and does not inhibit potential
cytochrome P450 enzymes such as CYP1A2, CYP2C19, CYP2C9, CYP2D6 and
CYP3A4. The molecule obeys PAINS and Brenk medicinal chemistry rules.
3.4 TARGET PREDICTION:
After the analysis the target prediction of the ligands Eritadenine,
Gallic acid, Ergosterol peroxide and Pleuran were given accordingly as
the pie charts for top 15 hits for Eritadenine, all estimates for Gallic
acid, top 15 hits for Ergosterol peroxide and all estimates for Pleuran
(Figures 10-13) and the respective log output table with known protein
complexes are given along with probability score with each binding to
estimated protein complexes, the output table of results for the
compounds are given in the supplementary file. As projected by the
output file the compounds may reach the target with high accuracy to
which it is targeted to. Whereas the target activities of Eritadenine,
Gallic acid, Ergosterol peroxide and Pleuran are sought in literature
and their validation is discussed in the discussion section to provide
the fact of target accuracy.
3.5 TOXICITY PREDICTION:
3.5.1 SYSTEMIC TOXICITY:
The systemic toxicity properties of the ligands eritadenine, gallic
acid, ergosterol peroxide and pleuran are tabulated in Table-13.
3.5.2 TOX21 PATHWAY:
The properties of the ligands which are studied for TOX21 pathway are
given in the Table-14 as follows:
3.5.3 TOXICOPHORE RULES:
The toxicophore rules of the ligands of interest are tabulated in
Table-15.