The 2D structures of A. indica molecules -Arachidic acid, Azadirachtin, Azadirachtin B, Azadirachtol, Azadiradione, Margosinolide, Melianin, Melianone, Nimbidinin, Nimbidiol, Nimbinene, Nimbiol, Nimbolide, Nimbolin A, Nimocin; and T. cordifolia molecules Berberine, Columbin, Cordifolide A, Jatrorrhizine, Kaempferol, Tinosponone, Tinosporinone; and antiviral molecule- Remdesivir were shown in Fig.1. Druggability of these molecules is found favorable through Lipinski’s Rule of Five. All 23 ligands qualify with no violation in Lipinski’s Rule. Table 1. These ligands docked with SARS-CoV–2
proteases viz. Spike protease (S) and Mpro protease and generated negative values for energies in Kcal/mol. Binding energy –5.0 Kcal/mol and above was considered as drug potential for preventing spike protease attaching cellular membrane and ACE2 interaction.
Best affinities with root mean square deviation (RMSD) obtained in the PyRx AutoDock Vina were recorded. Among the 9 poses from each ligand best affinity of docking with RMSD was taken for analysis. All ligands were docked successfully with Mpro (6LU7) protease and affinities were found between –4 4 Kcal/mol and –8.2 Kcal/mol. Phytochemicals from A. indica, Kaempferol and Azadirachtin B showed high affinities with –7.8Kcal/mol, and –7.7Kcal/mol respectively.
Table 1. Molecules with Lipinski Rule of Five
Sl No.
|
Ligand
|
Molecular Formula
|
Mass (<500
Dalton)
|
Hydr ogen Bond Don or (<5)
|
Hydro gen Bond Accep tors (<10)
|
LogP (<5)
|
Molar Refractivit y (Between 40-130)
|
1.
|
Arachidic acid
|
C20H40O2
|
312.000
|
1
|
2
|
7.112
|
96.415
|
2.
|
Azadirachtin
|
C34H44O9
|
720.000
|
3
|
16
|
-0.203
|
164.279
|
3.
|
Azadirachtin B
|
C35H44O16
|
720.000
|
3
|
16
|
-0.203
|
164.2796
|
4.
|
Azadirachtol
|
C28H36O13
|
580.000
|
4
|
13
|
-1.611
|
130.266
|
5.
|
Azadiradione
|
C28H34O5
|
450.000
|
0
|
5
|
5.41
|
123.172
|
6.
|
Jatrorrhizine
|
C20H20NO4
|
466.000
|
0
|
7
|
3.743
|
119.387
|
7.
|
Kaempferol
|
C15H10O6
|
286.000
|
4
|
6
|
2.305
|
72.385
|
8.
|
Margosinolide
|
C27H32O8
|
484.000
|
1
|
8
|
2.257
|
121.470
|
9.
|
Melianin
|
C41H58O9
|
694.000
|
2
|
9
|
6.437
|
186.645
|
10.
|
Melianone
|
C30H46O4
|
470.000
|
1
|
4
|
6.061
|
131.919
|
11.
|
Nimbidinin
|
C26H34O6
|
442.000
|
3
|
6
|
2.489
|
115.907
|
12.
|
Nimbidiol
|
C17H22O3
|
274.000
|
2
|
3
|
3.768
|
77.193
|
13.
|
Nimbinene
|
C28H34O7
|
482.000
|
0
|
7
|
4.523
|
126.188
|
14.
|
Nimbiol
|
C18H24O2
|
272.000
|
1
|
2
|
4.371
|
80.265
|
15.
|
Nimbolide
|
C27H30O7
|
466.000
|
0
|
7
|
3.743
|
119.387
|
16.
|
Nimbolin A
|
C39H46O8
|
642.000
|
0
|
8
|
7.049
|
173.612
|
17.
|
Nimocin
|
C33H38O4
|
498.000
|
0
|
4
|
7.532
|
142.874
|
18.
|
Berberine
|
C20H18NO4
|
336.000
|
0
|
5
|
2.307
|
93.548
|
19.
|
Columbin
|
C20H22O6
|
358.000
|
1
|
6
|
2.532
|
88.555
|
20.
|
Cordifolide A
|
C28H38O12S
|
336.000
|
0
|
5
|
2.307
|
93.548
|
21.
|
Tinosponone
|
C19H22O5
|
330.000
|
1
|
5
|
2.836
|
84.739
|
22.
|
Tinosporinone
|
C19H18O6
|
470.000
|
1
|
4
|
6.061
|
131.919
|
23.
|
Remdesivir
|
C27H35N6O8P
|
602.000
|
4
|
10
|
1.930
|
213.36
|
Other molecules docked with 6LU7 protease showed good affinities; Azadiradione –7.6, Margosinolide –7.6, Melianin–7.5, Nimbolide –7.4, Azadirachtol –7.2, Nimbidin–7.2, Jatrorrhizine–7.1, Nimbidiol –7.1, Azadirachtin–7, Melianone–6.8, Nimocin–6.6, Nimbinene- 6.4, Nimbiol –6.4, Nimbolin –5.1kcal/mol.
However, Arachidic acid showed –4.4kcal/mol affinity. Molecules from T. cordifolia showed good affinities as Cordifolide A –8.2, Tinosponone –7.4, Columbin –7.3, Berberin–6.8, Tinosporinone –6.5. Antiviral drug Remdesivir showed an affinity with –7. Spike protein 6VXX was docked with all ligands and showed good binding energies between –5.6 Kcal/mol and –10.3Kcal/mol. Among these, Cordifolide A and Nimocin showed high affinities with –10.3Kcal/mol and –9.8 Kcal/mol respectively. Other molecules from A. indica produced good affinities; Nimocin –9.8, Azadirachtin B –9.6, Nimbolin–9.4, Nimbolide –9.3, Nimbinene–9.2, Margosinolide –9.1, Melianone–9, Azadiradione–8.9, Melianin –8.9, Nimbidinin –8.7, Nimbiol –8.7, Azadirachtol –8.6, Jatrorrhizine –8.5, Kaempferol –8.4, Azadirachtin –8.2, Nimbidiol–7.7, Arachidic acid –5.6, Molecules from T. cordifolia showed affinities; Tinosponone –8.9, Columbin –8.3, Berberine –8, Tinosporinone –7.6 Antiviral drug Remdesivir showed an affinity with –7.6Kcal/mol. Table 2
Table 2. Receptors with Ligand Affinities and Root Mean Square Deviation (RMSD)
SL No
|
Ligand
|
6LU7
|
6VXX
|
Bonding Affinity kcal/mol
|
RMSD
hd
|
RMSD
ld
|
Bonding Affinity kcal/mol
|
RMSD
hd
|
RMSD
ld
|
1.
|
Arachidic acid
|
-4.4
|
0
|
0
|
-5.6
|
0
|
0
|
2. `
|
Azadirachtin
|
-7
|
0
|
0
|
-8.2
|
0
|
0
|
3.
|
Azadirachtin B
|
-7.7
|
0
|
0
|
-9.6
|
0
|
0
|
4.
|
Azadirachtol
|
-7.2
|
0
|
0
|
-8.6
|
0
|
0
|
5.
|
Azadiradione
|
-7.6
|
0
|
0
|
-8.9
|
0
|
0
|
6.
|
Berberine
|
-6.8
|
0
|
0
|
-8
|
0
|
0
|
7.
|
Columbin
|
-7.3
|
0
|
0
|
-8.3
|
0
|
0
|
8.
|
Cordifolide A
|
-8.2
|
0
|
0
|
-10.3
|
0
|
0
|
9.
|
Jatrorrhizine
|
-7.1
|
0
|
0
|
-8.5
|
0
|
0
|
10.
|
Kaempferol
|
-7.8
|
0
|
0
|
-8.4
|
0
|
0
|
11.
|
Margosinolide
|
-7.6
|
0
|
0
|
-9.1
|
0
|
0
|
12.
|
Melianin
|
-7.5
|
0
|
0
|
-8.9
|
0
|
0
|
13.
|
Melianone
|
-6.8
|
0
|
0
|
-9
|
0
|
0
|
14.
|
Nimbidinin
|
-7.2
|
0
|
0
|
-8.7
|
0
|
0
|
15.
|
Nimbidiol
|
-7.1
|
0
|
0
|
-7.7
|
0
|
0
|
16.
|
Nimbinene
|
-6.4
|
0
|
0
|
-9.2
|
0
|
0
|
17.
|
Nimbiol
|
-6.4
|
0
|
0
|
-8.7
|
0
|
0
|
18.
|
Nimbolide
|
-7.4
|
0
|
0
|
-9.3
|
0
|
0
|
19.
|
Nimbolin
|
-5.1
|
0
|
0
|
-9.4
|
0
|
0
|
20.
|
Nimocin
|
-6.6
|
0
|
0
|
-9.8
|
0
|
0
|
21.
|
Remdesivir
|
-7
|
0
|
0
|
-7.6
|
0
|
0
|
22.
|
Tinosponone
|
-7.4
|
0
|
0
|
-8.9
|
0
|
0
|
23.
|
Tinosporinone
|
-6.5
|
0
|
0
|
-7.6
|
0
|
0
|
Conventional Hydrogen bonds, van der Waals, carbon bonds, Pi Alkyl, etc. with amino acids in 2D are depicted in Fig.2 and Fig 3. Ligands docked with Mpro protein residues having H bonds are noted as Kaempferol SER144, Azadirachtin B LEU287, TYR239, Azadiradione MET276, ARG131, Margosinolide LYS137, LEU287, Melianin THR111, Nimbolide, SER158, LYS102, Azadirachtol LEU271, Nimbidinin GLN110, SER158, Jatrorrhizine
LEU271, Nimbidiol THR190, ARG188, Azadirachtin ARG131, THR199, LEU272, Remdesivir THR190, GLU166, ASN142, CYS145, GLY143, Melianone LYS5, GLN127, Nimocin LYS5, Nimbinene ASN142, GLU166, Nimbiol LYS102, SER158, Nimbolin GLN127, LYS5, Arachidic acid THR111, GLN110, ASP295, Cordifolide A LYS137, ASP197, ASN238, THR199, Tinosponone GLN110, ER158, LYS102, Columbin THR26,
Berberine LEU287, Tinosporinone GLY143, GLY166.
Similarly, ligands docked with spike protein and their target residues noted as Nimocin TRY756, THR C998, THR B998, Azadirachtin B THR430, LEU518, LEU517, SER975,
Nimbolin ARG765, Nimbolide GLN1036, ARG1107, Nimbinene ASN B1023, ASN C 1023, Margosinolide TYR 756, ARG995, THR998, TYR C756, ASP994, Melianone GLN1113, VAL1122, Azadiradione ARG995, TYR756, Melianin SER50, HIS49, THR761, LYS304, Nimbidinin THR998, TYR756, Nimbiol LEU517, PHE515, Azadirachtol ARG983, THR430, ASP428, SER514, Jatrorrhizine GLY314, ILE666, LYS733, Kaempferol TRP886, Azadirachtin THR723, THR1027, Nimbidiol ARG1107, ASN1108, TYR904, Remdesivir ARG139, ALA1020, Arachidic acid GLY744, TYR741, Cordifolide A GLN414, THR415, GLU988, TYR369, LYS417, Tinosponone TYR904, LYS1038, HIS1048,
GLY1036, Columbin THR998, TYR756, Berberine ASN764, Tinosporinone LYS1028, GLN784 Table 3, Table 4, Fig 4, Fig 5