8.0 Discussion and conclusion 1965shodhganga.inflibnet.ac.in/.../43802/11/11_chapter8.pdf · 2018-07-03 · 8.0 Discussion and conclusion In the Type 1 diabetes or autoimmune diabetes,

8.0 Discussion and conclusion

In the Type 1 diabetes or autoimmune diabetes, the beta cells that produce insulin are

slowly destroyed by the body's own immune system. Willy Gepts(1965) described the

pathology of the endocrine pancreas in human diabetes and identified key morphological

differences between the types and stages of the disease. He is best known for showing that

insulitis—inflammatory infiltrates in and around pancreatic islets which is characteristic of

recent-onset juvenile diabetes. There may be a partial overlap in etiology between T1D and

T2D which is masked by hyperglycemia in T2D and autoimmune destruction of islets in T1D

Herbal flavonoids that are present in various Ayurvedic preparations are known to

be potent antioxidants and thus prevent T1D in NOD mice. Further, animal and clinical

studies suggest that moderate immunosuppression in newly diagnosed T1DM patients can

prevent autoimmunity and it has been chosen as the key background support for the current

research pursuit.

A particular flavonoid compound, 2, 4- dimethoxy iso flavanonehas been identified

from Cyperus rotundus by a series of wet laboratory experiments including column

chromatography, TLC and GC-MS. Along with other known compounds of Cyperus rotundus

such as alpha cyperone, cyerene, cyperotundone, kubosone and sugeonol and Curcumin from

Curcuma longa , docking experiments were performed to identify the most potential inhibitor

compound for all of the selected protein and immune agents associated with the T1D

pathway.

ADMET studies revealed the drug likeliness of the ligands,being screened by the

Lipkiski Filters, Toxicity study, done as per Cramer‘s rule, using the tool Toxtree 2.5.4, and

Qikprop of the Schrodinger software.

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These establish that the ligands, Alphacyperone, Cyperotundone, curcumin, 2, 4 –

dimethocy isoflanone, Kobusone and sugeonol are the best ligands.

Toxicity study, carried out as per Cramer‘s rule, using the tool Toxtree 2.5.4 awards

a High Class- Class III for the ligands Alphacyperone, Cyperotundone, curcumin, 2, 4 –

dimethocy isoflanone, Kobusone and sugeonol and a low class for the ligand Cyperene.

The study carried out using the Qikprop module of the Schrodinger software also

reveals an outcome similar to the above studies and confirms that the ligands, Alphacyperone,

Cyperotundone, curcumin, 2, 4 –dimethocy isoflanone, Kobusone and sugeonol are the best

out of the seven that were included in this study.

The Induced Fit Docking experiments performed, help to demonstrate the binding

energy of various ligand receptor interactions and thus confirm the utility and future worth of

the present research. It has also been established that the notable outcome of ADMET and

Ligand- receptor interaction surveys using various insilico tools, would otherwise be

expensive and time consuming when carried out in the wet laboratory.

Induced Fit Docking (IFD) experiments were performed using the Mastero platform of

the Schrodinger tool 9.2 version. IFD studies were carried out between all ten selected protein

targets and the seven ligands. In IFD, the target is induced to provide a best 3 dimensional fit

for the ligand. The best outputs were selected and analysed to identify the best Drug –

Receptor combinations.

In the usual docking studies, ligands are docked into the binding site of a receptor

where the receptor is held rigid and the ligand is free to move. This could not always be true,

because in the living system, many proteins undergo three dimensional structural

modifications. They experience either side-chain or backbone movements, or both


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dependingupon the ligand binding to them. These changes allow the receptor to alter its

binding site so that it more closely conforms to the shape and binding mode of the ligand. This

is often referred to as ―induced fit‖ and is one of the main complicating factors in structure-

based drug design.

The practical applications of IFD fall into three main categories:

o Generation of an accurate complex structure for a ligand known to be active but that cannot be

docked in an existing (rigid) structure of the receptor.

o Avoid false negatives (poorly scored true binders) in virtual screening experiments, where

instead of screening against a single conformation of the receptor, additional conformations

obtained with the induced fit protocol are used.

o A better ligand – receptor interaction study is possible, IFD score provides a better disclosure

of their binding energy, which is very significant.

HLA class II histocompatibility antigen, DP (PDB ID: 3LQZ)

This protein (Dai, S. et al., 2010), on docking with Alpha cyperone, formed one H-

bond side chain with the residue Tryptophan 128 of Chain A. it is also noteworthy that the

ligand is embedded in the pocket formed by the residues Valine 149, Isoleucine 146,

Metheionine 158, Leucine 156 and Valine 114 of Chain B, and Phenylalanine 92, Isoleucine

106, Leucine 105, Glutamin 181 and Proline 93 of Chain A. this is evident from the IFD

output number11 of this particular ligand.

The Glide Energy for this output is -28.43 and the Glide Score is -5.08 which are

significant.


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The binding site was formed by a gird box containing the reisdues:

A:104,A:176,A:179,A:94,A:96,A:97. The same protein, on docking with Cyperene on the

same Binding site, obtained a Glide Energy of -25.13 and a Glide Score of -3.44. Output

number 9 shows the ligand embedded in the pocket formed by Glutamate 95, Proline 93,

Asparginine 103 (polar residue), Valine 97and Proline 96 of Chain A and Histidine 116,

Threonine 118 and Arginine 96 of Chain B.

When the binding site was changed to enclose A:114, A:115, A:116, A:13,A:16,

A:20, A:21, A:35, A:81, A:82 for the ligand Cyperene, it obtained a Glide Energy of -29.34

and a Glide Score of -4.83 as per output number 3.

Induced Fit Docking of 3LQZ and Kobusone at the binding site formed by the

residues A:114, A:115, A:116, A:13, A:16, A:20, A:21, A:35, A:81, A:82 shows that

significant H-bonds were formed with the residues Leucine 36, Glycine 20 and Threonine 19

of Chain A as per output number 8 (Glide Score -6.91, Glide Energy -27.7) and with

tryptophan 168 of chain A and Serine 3 of Chain B.

Induced Fit Docking of 3LQZ and Ligand sugeonol at the binding site: A:114,

A:115, A:116, A:13,A:16, A:20, A:21, A:35, A:81, A:82 showed H-bond backboned formed

with Threonine 19 and Leucine 36, and a H-bond side chain was formed with Asp37 as per

output 9 (Glide Score -4.35, Glide Energy -31.86). The output 11showed H-bond backbone

formed with Leucine36 and Valine 34 (Glide Score -4.81, Glide Energy -32.67).

Induced Fit Docking of 3LQZ and Ligand curcumin at the binding Site formed by

A:114, A:115, A:116, A:13, A:16, A:20, A:21, A:35, A:81, A:82: Output 5 shows H-bond

backbone with Leucine 36, Serine 135 and H-bone side chain with Asparginine 67(Glide


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Score -5.7, Glide Energy -42.64).Output 10 shows H-bond backbone with Leucine 117 and H-

bond side chain with Glu 21(Glide Score -4.19, Glide Energy -35.32).

Induced Fit Docking of 3LQZ and Ligand 2, 4- dimethoxy iso flavanone at the

binding Site formed by A:114, A:115, A:116, A:13, A:16, A:20, A:21, A:35, A:81, A:82:

Output 8 shows H-bond backbone with Valine 119 and bound by Threonine 120, Asparginine

118, Proline 18, Leucine 117, Lysine 147 and Histidine 149. The highest Glide Score was -

3.38, and the corresponding Glide Energy was -26.56. Output 16 shows the ligand embedded

in the pocket formed by Aspartate 37, Threonine 19, Leucine 36 and Asparginine 67.

The IFD score is the highest for Alpha Cyperone (-825.8425197) and the 2nd

highest

for 2, 4- dimethoxy iso flavanone (-817.3815591).

But based on the H-bond score and the Glide Energy, Curcumin could be

suggested as the best ligand for this protein and the 2nd

best would be2, 4- dimethoxy iso

flavanone.

Phogrin: Protein tyrosine phosphatase- PTRN2beta (PDB ID: 2QEP)

Ligand binding sites for alphacyperone, Cyperene, Cyperotundone, sugeonol,

Kobusone and 2, 4- dimethoxy iso flavanone: includes A:755, A:756, A:757, A:760, A:762,

A:766, A:777, A:778, A:779, A:780, A:782, A:982, A:986, A:987, A:988.

Ligand binding sites for curcumin includes the residues A:755, A:756, A:757, A:758,

A:759, A:760, A:761, A:762, A:763, A:764, A:765, A:766, A:767, A:768, A:769, A:770,

A:771, A:772, A:773, A:774, A:775, A:776, A:777

Induced Fit Docking of 2QEP (Barr, A.J. et al., 2009) and Ligand Alpha cyperone:

Output 3 shows ligand forming an H-bond with Arginine 982 and Cystine 753(Glide Score -

2.51, Glide Energy -23.75). Output 9 shows H-bond with Serine 762. Output 8 shows the


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ligand embedded in the pocket bound by Alanine 765, Leucine 780, Serine 762 and

Glutamine 766.

Induced Fit Docking of 2QEP and Ligand Cyperene: Output 3 shows ligand

embedded in the pocket formed by Serine 776, Alanine 778, Valine 779 and Cystine 753.

Output 12 shows ligand embedded in the pocket formed by Alanine 778, 754,

Glutamine 756, Proline 986, Tyrosine 755 and Valine 779.

Output 16 shows ligand embedded in the pocket formed by Alanine 754, Cystine

753, Proline 986, Glycine 987 and Arginine 985, with an H-bond with Arginine 982(Glide

Score -2.02, Glide Energy-26.58).

Induced Fit Docking of 2QEP and Ligand Cyperotundone: Output 3 shows ligand

embedded in the pocket formed by Alanine 757, Glutamine 756, Asparginine 760, Proline

759, 986, Serine 761, and Tyrosine 782, with an H-bond backbone with Glycine 987(Glide

Score -3.11, Glide Energy-22.6 and H-bond score -0.7).

Output 5 is similar to output 3 with Glide Score -3.4, Glide Energy -24.37 and H-

bond score -0.7.

Output 9 shows ligand embedded in the pocket formed by Alanine 757, Asp 983,

Arginine 982, Leucine 981, Glutamine 984, Proline 986 and Tyrosine 782, (Glide Score -2.64,

Glide Energy -27.77)

Output 10 shows ligand embedded in the pocket formed by Proline 986, Alanine 949,

Glycine 987, Arginine 982, Glutamine 990, 756 and Valine 779.

Induced Fit Docking of 2QEP and Ligand Kobusone: Output 6 shows a single H-

bond backbone formed with Glycine 987, while output 7 shows an H-bond backbone with

Alanine 757 and an H-bond side chain formed with Arginine 982. Output 11 shows a single


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H-bond backbone formed with Alanine 757 and output 15 shows a single H-bond backbone

formed with Glycine 987.

Induced Fit Docking of 2QEP and Ligand Sugeonol: Output 4 shows two H-bond

backbones formed with Glycine 987 and Alanine 757(Glide Score-3.1, Glide Energy -27.02,

H-bond score -1.33). Output 15 shows two H-bond backbones formed with Glycine 987 and

Tyrosine 755 (Glide Score -3.77, Glide Energy -25.96, H-bond score -1.11).

Induced Fit Docking of 2QEP and Ligand Curcumin: Output 4 shows two H-bond

side chains formed with Arginine 786 and Arginine 767, and an H-bond backbone formed

with Asp 783(Glide Score -2.86, Glide Energy -32.06, H-bond score -2.05). Output 5 shows

two H-bond side chains formed with Arginine 786 and Arginine 767, and H-bond backbones

formed with Aspartate 783 and Glutamine 766(Glide Score -2.78, Glide Energy -33.88, H-

bond score -1.78). Output 6 shows two H-bond side chains formed with Arginine 786 and

Arginine 767(Glide Score -2.08, Glide Energy -30.08, H-bond score -1.34).

Induced Fit Docking of 2QEP and Ligand 2, 4- dimethoxy iso flavanone: Output 4

shows a single H-bond backbone formed with Glycine 987(Glide Score -4.26, Glide Energy -

31.32, H-bond score -1.2). Output 7 shows a single H-bond backbone formed with Alanine

757. Output 8 shows a single H-bond backbone formed with Serine 762 and an H-bond side

chains formed with Asparginine 760. The ligand is exposed to the residues Alanine 778,

Glutamine 756 and Glycine 987(Glide Score -4.82, Glide Energy -29.12, H-bond score -1.29).

Output 11 shows a single H-bond backbone formed with Alanine 757. Output 17 shows a

single H-bond side chain formed with Arginine 786, ad surrounded by Arginine 767, Valine

764, Leucine 788 and Asp 783.


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The IFD score is the highest for Ligand: 2, 4- dimethoxy iso flavanone, which is

-1310.021858, which also has the highest Glide score, and therefore could be suggested to

be the best ligand for this protein target, Phogrin.

HUMAN B7-1/CTLA-4 CO-STIMULATORY COMPLEX: CD80 (PDB ID:

1I8L)

CD80 Stamper, (Stamper, C.C. et al., 2001) was subject to IFD at the Binding Site

formed by the residues A: 161, A:40, A:50, A:52, A:57, A:58, A:70, A:71 for all the 7

ligands.

IFD of Alpha cyperone as per output 2 showed a H-bond formed with Lysine 6 of

chain B. the ligand was found embedded within the pocket formed by the residues Asp 60,

Valine 68 and Threonine 13 of chain B and Asparginine 55 of chain A. output 4 shows the

ligand enclosed by the residues Arginine 56 and Isoleucine 49 of chain A, and Serine 66,

Asparginine 63, 64 and Asp 60 of chain B. output 9(Glide Score -3.53, Glide Energy -27.17)

and 11(Glide Score -3.52, Glide Energy -27.18) are similar to output 2(Glide Score -3.44,

Glide Energy -27.17). Output 15 shows a H-bond formed between the ligand and the residue

Asparginine 55 of chain A. it also shows the ligand closely bound by the residues Serine 66,

Threonine 13, 62 and Asp 60.

IFD of Cyperene and CD80, as per output 6 shows the ligand included within Serine

66, Asp 60 and Asn 63 of chain B. Output 13 shows a boundary by the residue Asparginine 55

in addition to the above 3 residues. Output 19 shows the ligand bound by the residues Valine

11, 68, Lysine 6, Threonine 13, 63, Serine 66, Aspartate 60, Asparginine 63 and Isoleucine 58

of chain B, and Isoleucine 58 and Phenylalanine 59 of chain A. Output 20 shows the ligand

surrounded by the residues Valine 68, 11, Threonine13, Serine 66 and


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Asparginine 63, Isoleucine 58 and Leucine 70 and Chain B, and Isoleucine 58, Leucine 70,

lysine 54 and Asparginine 55 of chain A.

IFD of Cyperotundone and CD80, as per output 1 shows residues, Arginine 56,

Methionine 47, Threonine 62 and Leucine 70 circumvent the ligand, and the ligand interacts

with the target by an H-bond with the residue, Isoleucine 58 of chain A(Glide Score -3.88,

Glide Energy -28.16, H-bond score -0.7). Output 4 shows an H-bond backbone formed with

Threonine 57 of chain A. Output 6 shows an H-bond backbone formed with Phenylalanine 59

of chain A. Output 11 shows an H-bond side chain formed with Lysine 6 of chain B, and the

ligand bound by Threonine 13, Valine 68, Asp60, Isoleucine 58, Serine 66 and Arginine

56(Glide Score -3.34, Glide Energy -24.76, H-bond score -0.35).

Induced Fit Docking of Kobusone and CD80, Output 16 shows an H-bond backbone

formed with Threonine 57 of chain A, and ligand exposure adjacent to residues Threonine13

and Valine 68 of chain B. Output 18 shows the ligand exposure adjacent to residues

Threonine13 and Alanine 12. The ligand is bound by the residues Isoleucine 69 and Valine 68

of chain B and Arginine 56 and Asparginine 55 of chain A.

Induced Fit Docking of Sugeonol and CD80: Output 1 shows an H-bond backbone

formed with Asparginine 55. Output 3 shows an H-bond backbone formed with Lysine 54.

Output 5 shows two H-bond backbones formed with Asparginine 63 and Threonine 62(Glide

Score -4.57, Glide Energy -33.27, H-bond score -1). Output 9 shows two H-bond backbones

formed with Asn 63 and Asp 60. Output 14 shows an H-bond side chain formed with Asp 60

of chain B(Glide Score -4.57, Glide Energy -33.27).

Induced Fit Docking of Curcumin and CD80: Output 1 shows two H-bond side

chains formed with Aspartate 60 and Lysine 6 of chain B, and H-bond backbones formed with


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Lysine 9 and Threonine 57 of Chain A(Glide Score -5.9, Glide Energy -47.12, H-bond score -

1.64). Output 2 shows two H-bond backbones formed with Lysine 9 and Threonine 57 of

Chain A and an H-bond side chain formed with Asp 60 of chain B.

Output 3 and Output 4 shows an H-bond side chain formed with Asp 60 of chain B,

and an H-bond backbone formed with Threonine 57 of Chain A. Output 6and Output 12 show

an H-bond side chain formed with Arginine73, Threonine 161 of chain A and Asp 60 chain B,

and an H-bond backbone formed with Lysine 8 of Chain A. Output 10 and Output 15 show an

H-bond side chain formed with Asp 60 of chain B, and an H-bond backbone formed with

Lysine 9 of Chain A. Output 13 shows an H-bond side chain formed with Asp 60 of chain B,

and an H-bond backbone formed with Lysine 9 and Threonine 161 of Chain A. Output 14

shows an H-bond side chain formed with Asp 60 and Lysine 9 of chain B, and an H-bond

backbone formed with Threonine 57 of Chain A. Output 16 shows an H-bond side chain

formed with Asp 60 of chain B, and an H-bond backbone formed with Threonine 57 and

Lysine 9 of Chain A.

Induced Fit Docking of 2, 4- dimethoxy iso flavanone and CD80: Output 2 shows an

H-bond side chain formed with Threonine 62 of chain B and shows the ligand exposure

adjacent to residues Isoleucine 49 and 58 of Chain A(Glide Score -3.59, Glide Energy -

31.31). Output 3 shows the ligand exposure adjacent to residues Threonine 57, Arginine 56

and Alanine 71 of Chain A. Output 15 (Glide Score -4.33, Glide Energy -30.68).shows the

ligand exposure adjacent to residues Threonine 57 and Alanine 71, and the ligand surrounded

by Isoleucine 58 and Leucine 70 of Chain A.


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The IFD score is the highest for Ligand: Curcumin -1362.562873, with

corresponding Glide score of -7.718823201. The IFD score is the second highest for Ligand:

alfacyperone -1356.211014 with corresponding Glide score of -3.742194387

The IFD score is the third highest for Ligand: 2, 4- dimethoxy iso flavanone -

1353.701694, which also has the highest Glide score -4.333410365. Considering the above

results of Glide score and Glide energy, 2, 4- dimethoxy iso flavanone could be suggested

to be the second best ligand for this protein target, CD 80, next to curcumin.

Heat Shock Protein 90 Alpha (PDB ID: 3HEK) was subject to Induced Fit

Docking at the Binding Site: B:BD0901(Chitra and Jeyanthi, 2011).

Induced Fit Docking of 3HEK with Ligand Alpha cyperone: Output 1 shows an H-

bond side chain formed with an water molecule bound on either side by Threonine 152 and

Glycine 97, and depicts the ligand exposure site adjacent to residues Asparginine 106, 51 and

Asp 102(Glide Score -5.66, Glide Energy -27.19). Output 10 shows a similar H-bond side

chain formed with an water molecule bound on either side by Threonine 152, 184 and Glycine

97, 183, and depicts the ligand exposure site adjacent to residues Asparginine 106, 51,

Methionine 98, and Asp 102, 54. The ligand is also bound by Glycine 137, Leucine 103 and

Glutamate 47(Glide Score -4.71, Glide Energy-36.34).

Induced Fit Docking of 3HEK and Ligand Cyperene: Output 1 shows the ligand to be

bound by a few water molecules, Aspartate 93, Alanine 55, Threonine 184, Methionine 98,

Valine 150, 186 and Asparagine 51.

Output 6 shows the ligand to be bound by a few water molecules, Aspartate 93, 54,

Alanine 55, Threonine 184, Valine 150, 186 and Asparagine 51. Output 8 shows the ligand to

be bound by a few water molecules, Aspartate 93, Alanine 55, Threonine 184, Methionine 98,


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Valine 150, 186, Serine 52, Asparagine 51 and Leucine 48(Glide Score -6.02, Glide Energy -

32.77). Output 11 shows the ligand to be bound by Aspartate 93, Alanine 55, Threonine 184,

154, Methionine 98, Valine 150, 186, Glycine 97, Serine 52, Asparagine 51 and a few water

molecules. Output 16(Glide Score, -5.75 Glide Energy -29.68) and Output 19 are similar to

Output 11.

Induced Fit Docking of 3HEK and Ligand Cyperotundone: Output 1 shows an H-

bond side chain formed with an water molecule of the protein and the Oxygen atom of the

ligand, bound on either side by Threonine 184 and Glycine 97, 183, Aspartate 93 and Alanine

55. Output 6 shows an H-bond side chain formed with an water molecule of the protein and

the Oxygen atom of the ligand, bound on either side by Threonine 184 and Glycine 97, 183,

Aspartate 93 and Alanine 55. Output 13 shows an H-bond side chain formed with an water

molecule of the protein and the Oxygen atom of the ligand, and the ligand bound by

Threonine 184, 152, Aspartate 54, Methionine 98, Leucine 103, 107, Phenylalanine 138 and

Asparginine 51. Output 14 shows an H-bond side chain formed with an water molecule of the

protein and the Oxygen atom of the ligand, and the ligand bound by Phenylalanine 138

,Methionine 98, Valine 186, Threonine 184, 152, Glycine 97, Isoleucine 91, 96, Aspartate 93,

102, Serine 52, Leucine 48, 107, and Asparginine 106(Glide Score -6.38, Glide Energy -

31.74). Output 17 shows an H-bond side chain formed with an water molecule of the protein

and the Oxygen atom of the ligand, and the ligand bound by Tryptophan 162, 139, Methionine

98, Alanine 55, Phenylalanine 138, Glycine 108, Aspartate 54, Leucine 107, and Asparginine

51(Glide Score -6.15, Glide Energy -28.42).

Induced Fit Docking of 3HEK and Ligand Kobusone at the binding site A: BD0901:

Output 14 shows an H-bond side chain formed with a water molecule of the protein and


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the Oxygen atom of the ligand, and another H-bond side chain formed with Lysine 58. the

ligand is bound by Phenylalanine 138, Valine 150, Serine 50, Leucine 103, Threonine 152,

Methionine 98, Aspartate 54, 102 and Asparginine 51(Glide Score -5.98, Glide Energy -30.2).

Output 20 shows a lot of similarity to Output 14 (Glide Score -5.44, Glide Energy -28.15).

Induced Fit Docking of 3HEK and Ligand sugeonol: Output 2 shows two H-bond

side chains formed with water molecules of the protein and the Oxygen atom and –OH group

of the ligand. The ligand is bound by Asparginine 51, Serine 52, Asparginine 106, Aspartate

93, 102, Alanine 55 and Leucine 58. Output 7 shows two H-bond side chains formed with

Oxygen atom of the ligand and Asparginine 106, and –OH group of the ligand and

Asparginine 51(Glide Score -7.96, Glide Energy -40.5). Output 8 shows an H-bond side chain

formed with an water molecule of the protein and the Oxygen atom of the ligand, and another

H-bond side chain formed with –OH group of the ligand and Asparginine 51. Output 9 shows

an H-bond side chain formed with an water molecule of the protein and the Oxygen atom of

the ligand, and the ligand is bound by Phenylalanine 138, Leucine 107, Methionine 98, Valine

150, Threonine 184, Isoleucine 96, Alanine 55, Valine 186 and Lysine 58. Output 10 shows

an H-bond side chain formed with Asparginine 106, and the ligand is bound by Threonine

184, Leucine 107, Valine 186, Asparginine 51, Serine 52, Aspartate 93, Alanine 55 and

Lysine 58(Glide Score -7.43, Glide Energy -38.83). Output 8 shows an H-bond side chain

formed with a water molecule of the protein and the –OH group of the ligand, and another H-

bond side chain formed with Oxygen atom of the ligand and Asparginine 51.

Induced Fit Docking of 3HEK and Ligand 6, curcumin: Output 7 shows an H-bond

side chains formed with O atom of the ligand and Threonine 184, and the ligand embedded in

a cell of 8 water molecules (Glide Score -7.87, Glide Energy -45.92).


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Induced Fit Docking of 3HEK and Ligand 2, 4- dimethoxy iso flavanone: Output 3

and Output 6 are similar and show an H-bond side chains formed with and Lysine 58.

Therefore, curcumin with IFD score -1014.463748 would be considered the best

ligand for this protein target, and Ligand 2, 4- dimethoxy iso flavanone, with IFD score

of -1009.68296878 would be the 2nd

best ligand for this protein.

Crystal structure of human tyrosine phosphatase PTPN22 (PDB ID: 2P6X) was

subject to IFD at the binding Site: A:248, A:249,A:250, A:251, A:296,A:297, A:298, A:299,

A:300, A:302, A:93, A:94, A:95. Induced Fit Docking of 2P6X and Ligand Alpha cyperone:

Output 3 shows an H-bond side chain formed with Glutamine 293. Output 4 is similar to

Output 3. Output 3 shows an H-bond side chain formed with Lysine 300. Output 3 shows an

H-bond side chain formed with Arginine 4. Output 16 does not have any significant

interactions.

Induced Fit Docking of 2P6X and Ligand Cyperene: Output 5 shows the ligand

bound by Tryptophan 210, 244, Leucine 289, 247, Glutamine 293, Arginine 4 and Valine 296.

Output 11 shows the ligand bound by Isoleucine 297, Lysine 300, Glutamine 293, Leucine 7

and Aspartate 2. Output 17 shows the ligand bound by Isoleucine 297, Leucine 7, Glycine

250, Glutamine 3, and Aspartate 2.

Induced Fit Docking of 2P6X and Ligand Cyperotundone: Output 1 shows an H-

bond side chain formed with Lysine 300. Output 2 shows an H-bond side chain formed with

Tryptophan 210. Output 3 is similar to Output 1. Output 5 shows an H-bond side chain

formed with Tryptophan 244. Output 5 and 8 are similar. Output 5 shows an H-bond side

chain formed with Tryptophan 244, and the ligand closely bound by Arginine 292. Output 12


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shows an H-bond side chain formed with Lysine 300 and the ligand closely bound by Valine

296 and Glutamine 293, similar to Output 1 and 3. Output 17 shows an H-bond side chain

formed with Tryptophan 244.

Induced Fit Docking of 2P6X and Ligand Kobusone: Output 2 shows two H-bond

side chains formed with Lysine 300 and Glutamine 293, and the ligand closely bound by

Valine 296, Arginine 4, Isoleucine 297 and Glycine 250. Output 3 shows two H-bond side

chains formed with Lysine 300 and Glutamine 293, and the ligand closely bound by Valine

296, Arginine 4, Isoleucine 297, Aspartate 249, Glutamine 3 and Glycine 250. Output 5

shows an H-bond back bone formed with Arginine 4. Output 14 shows two H-bond side

chains formed with Glutamine 293 and Histidine 301, and the ligand closely bound by Lysine

300, Isoleucine 297, Glycine 250 and Valine 296. Output 16 shows two H-bond side chains

formed with Glutamine 293 and Lysine 300, and the ligand closely bound by Histidine 301,

Isoleucine 297, Glycine 250 and Valine 296.

Induced Fit Docking of 2P6X and Ligand sugeonol: Output 1 shows an H-bond side

chain formed with –OH group of the ligand and Arginine 292. Output 3 shows an H-bond side

chain formed with –OH group of the ligand and Tryptophan 210 and another H-bond side

chain formed with Oxygen atom of the ligand and Tryptophan 244. Output 15 does not have

much significant interactions. Output 3 shows an H-bond side chain formed with Oxygen

atom of the ligand and Histidine 301. Output 17 shows two H-bond side chains formed with

Lysine 300 and Glutamine 293, and an H-bond Backbone formed with Lysine 248.

Induced Fit Docking of 2P6X and Ligand curcumin: Output 2 shows two H-bond

side chains formed with Lysine 300 and Glutamine 293, and an H-bond Backbone formed

with Arginine 213(Glide Score -8.16, Glide Energy -45.78). Output 3 and 2 are similar.


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Output 7 shows an H-bond side chain formed with Tryptophan 244 and an H-bond Backbone

formed with Arginine 213.

Induced Fit Docking of 2P6X and Ligand 2, 4- dimethoxy iso flavanone: Output 9

shows an H-bond side chain formed with Lysine 300. Output 16 the ligand closely bound by

Arginine 213, Tryptophan 244 and Lysine 248(Glide Score -5.28, Glide Energy -28.68).

The IFD score is the highest for Ligand curcumin -1368.195479 and the IFD

score is second highest for 2, 4- dimethoxy iso flavanone -1364.142302. Thus, considering

the IFD score, Glide score and the various ligand interactions, Curcumin could be

suggestive as the best ligand and the second best would be 2, 4- dimethoxy iso flavanone.

IL-7Rα (PDB ID: 3DI3) was subject to Induced Fit Docking at the Binding sites:

B:151, B:175, B:176, B:178, B:179, B:180, B:181, B:206, B:207, B:208. (McElroy, C.A. et

al., 2009)

Induced Fit Docking of 3DI3 and Ligand Alpha cyperone: output 3 shows an H-bond

backbone formed with Glutamine 151. Output 5 shows an H-bond side chain formed with

Tyrosine 149. Output 155 shows an H-bond side chain formed with Arginine 207.

Induced Fit Docking of 3DI3 and Ligand Cyperene did not yield any significant

results.

Induced Fit Docking of 3DI3 and Ligand Cyperotundone: Output 16 shows an H-

bond side chain formed with Lysine 157. Output 17 also shows an H-bond side chain formed

with Lysine 157, but the interactions with the surrounding residues slightly differ from that of

output 16.

Induced Fit Docking of 3DI3 and Ligand Kobusone: Output 2 shows an H-bond side

chain formed with Lysine 153. Output 4 shows an H-bond side chain formed with Tyrosine


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181. Output 5 also shows an H-bond side chain formed with Tyrosine 181 but the interactions

with the surrounding residues slightly differ from that of output 4. Output 13 shows an H-

bond side chain formed with Glutamine 176.

Induced Fit Docking of 3DI3 and Ligand Sugeonol: Output 2 shows three H-bond

side chains formed with Lysine 157, Glutamine 151 and Threonine 159. Output 5 shows two

H-bond side chains formed with Tyrosine 181, and Lysine 157. Output 6 shows two H-bond

side chains formed with Tyrosine 181 and Threonine 159. Output 9 also shows two H-bond

side chains formed with Tyrosine 181 and Lysine 157 as in Output 5, but the interactions with

the surrounding residues slightly differ.

Induced Fit Docking of 3DI3 and Ligand curcumin: Output 1 shows two H-bond

backbones formed with Tyrosine 205, and Valine 117, and an H-bond side chain with

Tyrosine 204. Output 8 shows three H-bond side chains formed with Tyrosine 204, Glutamate

152 and Arginine207, and an H-bond backbone with Valine 117.

Induced Fit Docking of 3DI3 and Ligand 2, 4- dimethoxy iso flavanone: Output 2

shows an H-bond side chain formed with Glutamine 176. Output 8 shows the ligand bound by

Valine 162, Lysine 174, Leucine 175, 157, Tyrosine 181, 149 and Threonine 159. Output 9

shows two H-bond side chains formed with Tyrosine 149 and Glutamine 176.

The ligand Cyperene demonstrated very poor docking ability with this protein, and

hence its results have not been considered. Among the other ligands, curcumin with and IFD

score of -688.9325436 would be the best and the 2nd

best would be 2, 4- dimethoxy iso

flavanone with an IFD score of -684.1093797

Phosphoinositide 3-kinase P110delta (PDB ID: 2X38 which supersedes 2WXE)

was subject to IFD at the ligand binding site A: IC82028 (Berndt, A. et al., 2010).


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Induced Fit Docking of 2X38 and Ligand alpha cyperone: Output 2 shows an H-bond

back bone formed with Valine 828, and the ligand is embedded in the pocket formed by the

residues Phenylalanine 778, Isoleucine 777, 825, 910, 776, 761, Methionine 900, Glutamate

826, Serine 831, Valine 827 and Threonine 833. Also 2 water molecules are present within 4

Amstrong radius of the ligand (Glide Score -7.58, Glide Energy -32.47). Output 12 shows an

H-bond side chain formed with an water molecule and the ligand is bound by Isoleucine 910,

Methionine 752, 900, Threonine 833, Aspartate 832, Tryptophan 860, Phenylalanine 908,

Isoleucine 777 and another water molecule. Output 13 and 12 are almost similar, with minor

variations (Glide Score -7.08, Glide Energy -33.65).

Induced Fit Docking of 2X38 and Ligand Cyperene: Output 1 shows the ligand

bound by the residues Proline 758, Methionine 752, Isoleucine 777, Valine 827, Tryptophan

860, Leucine 829, Phenylalanine 751, Lysine 708 and Aspartate 753. Output 4 shows the

ligand docked into a pocket formed by two water molecules and enclosed by, Tryptophan 760,

Valine 827, Tyrosine 813, Serine 831, Methionine 900, Isoleucine 777, 825, 910, Aspartate

911 and Methionine752 (Glide Score -5.64, Glide Energy -28.1). Output 5 shows the ligand

docked into a pocket enclosed by Serine 831, Methionine 900, Aspartate 911, Valine 827,

Proline 758, Tryptophan 760 and Methionine 752. Output 6 shows the ligand docked into a

pocket enclosed by Tryptophan 760, Methionine 900, Leucine 759, Isoleucine 777, 910,

Proline 758, Methionine 752, Phenylalanine 751, threonine 833 and 750. Output 13 shows the

ligand docked into a pocket formed by one water molecule Aspartate 911, Lysine 779, Proline

758, Lysine 708, threonine 750, Tryptophan 760, Isoleucine 777, 910, Methionine 900,

Aspartate 832 and Methionine 752. Output 20 shows the ligand docked into


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a pocket formed by one water molecule Methionine 752, 900, Phenylalanine 908, Valine 828,

827 a water molecule, Leucine 829 and Serine 831.

Induced Fit Docking of 2X38 and Ligand Cyperotundone: Output 1 shows an H-

bond side chain formed with an water molecule and the ligand is bound by another water

molecule, Isoleucine 910, Methionine 752, 900, Threonine 833, Aspartate 911, 832, Lysine

779, Phenylalanine 908, 751, Valine 828, Isoleucine 777, Proline 758, Serine 831 and

Tryptophan 860(Glide Score -5.94, Glide Energy -30.38). Output 2, 3, 6, 7 and 10 also show

an H-bond side chain formed with an water molecule and the ligand is bound by another water

molecule, but the interactions with the surrounding residues vary significantly.

Induced Fit Docking of 2X38 and Ligand Kobusone: Output 2 shows an H-bond side

chain formed with a water molecule and a H-bond back bone formed with Valine 828. The

ligand is bound by another water molecule, Isoleucine 910, 777, Phenylalanine 908, Valine

827, Serine 831, Tryptophan 860, Methionine 752, 900, Proline 758, Aspartate 911 and

Asparginine 898 (Glide Score -7.34, Glide Energy -30.61). Output 26, 12 and 18 show an H-

bond side chain formed with a water molecule and the ligand bound by another water

molecule, Methionine 752, Serine 831, Tryptophan 860 and Valine 827. The interactions with

the other surrounding residues are insignificant.

Induced Fit Docking of 2X38 and Ligand Sugeonol: Output 1 shows an H-bond

backbone formed with Valine 828. The ligand is bound by two water molecules, Isoleucine

777, Valine 827, Serine 831, Methionine 752, 900, Aspartate 832, Isoleucine 825, Threonine

833 and Proline 758. Output 2 shows an H-bond side chain formed with a water molecule and

–OH group of ligand. Output 4 shows 3 H-bond side chains formed with a water molecule,

Aspartate 911 and Threonine 833. Output 5 shows 3 H-bond side chains formed with


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Aspartate 911 and interactions with two water molecules. Output 6 shows an H-bond side

chain formed with a water molecule and –OH group of the ligand. Output 9 shows an H-bond

side chain formed with a water molecule and O atom of the ligand, and interactions of water

molecules with residue Aspartate 911. Output 11 shows an H-bond side chain formed with a

water molecule and –OH group of the ligand and interactions of water molecules with residue

Aspartate 911. Output 15 shows an H-bond side chain formed with a water molecule and –OH

group of the ligand and interactions of water molecules with residue Aspartate 911. It also

shows an H-bond backbone formed with Valine 828.

Induced Fit Docking of 2X38 and Ligand curcumin: Output 2 shows two H-bond

side chains formed with water molecules and an H-bond back bone formed with Valine 828.

Output 5 shows 3 H-bond side chains formed with, a water molecule, Lysine 708 and

Threonine 750, and an H-bond back bone formed with Valine 828. Output 6 shows two H-

bond back bones formed with Valine 828 and Serine 831. Output 7 shows 3 H-bond side

chains formed with, a water molecule, Threonine 833 and Aspartate 832. Output 9 shows 3 H-

bond side chains formed with two water molecules and Threonine 750, and an H-bond back

bone formed with Valine 828 (Glide Score -10.48, Glide Energy -54.02).

Induced Fit Docking of 2X38 and Ligand 2, 4- dimethoxy iso flavanone: Output 2

shows an H-bond side chain formed with a water molecule and O atom of the ligand, and

interactions of water molecules with residue Aspartate 911. It also shows an H-bond back

bone formed with Valine 828. Output 8 shows an H-bond side chain formed with a water

molecule and O atom of the ligand, and interactions of water molecules with residue

Aspartate 911. Output 9 and 8 have more similarities and slight variations in the interaction

with the surrounding residues (Glide Score -8.13, Glide Energy -39.49).


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As per the IFD score -1942.607512 for 2, 4- dimethoxy iso flavanone, it can be

considered as the second best, next to curcumin which has an IFD score of -1946.493036.

The second highest Glide score of -8.13 as per Output 9 of 2, 4- dimethoxy iso flavanone,

also substantiates this conclusion. Therefore the third best ligand for this target could be

Kobusone.

IFD of Dipeptidyl peptidase 4 – (PDB ID: 2RIP) at the ligand binding site occupied

by 34Q800 [(3R,4R)-4-(pyrrolidin-1-ylcarbonyl)-1-(quinoxalin-2-ylcarbonyl)pyrrolidin-3-

amine] of Chain A (Corbett, J.W. et al., 2007)

Induced Fit Docking of 2RIP and Ligand Alpha cyperone: Output 5 shows the ligand

to be bound by the residues Glycine 549, tyrosine 662, 631, 547, Asparginine 710, Arginine

125, Glutamate 205 and Tryptophan 201.

Induced Fit Docking of 2RIP and Ligand Cyperene: Output 9 shows the ligand to be

bound by the residues Tyrosine 547, Phenylalanine 357, Arginine 358, Serine 209, Valine 207

and Glutamate 206.

Induced Fit Docking of 2RIP and Ligand Cyperotundone: the binding site was

changed for this ligand (to include the following residues A:242, A:243, A:245, A:333,

A:343, A:366, A:368, A:370) in order to study the difference in ligand interaction in yet

another ligand pocket.

Output 3 shows an H-bond side chain formed with Tryptophan 154 and Oxygen atom

of the ligand. Output 7, 12 and 17 show an H-bond side chain formed with Serine 212 and

Oxygen atom of the ligand(Glide Score -4.7, Glide Energy -26.86). Output 9 and 14 show an

H-bond back bone formed with Valine 303 and Oxygen atom of the ligand. Output 15 shows

an H-bond side chain formed with Tryptophan 215 and Oxygen atom of the ligand.


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Induced Fit Docking of 2RIP and Ligand kobusone: Output 1 and 6 show an H-bond

side chain formed with Tyrosine 631 and Oxygen atom of the ligand. Output 5 shows two H-

bond side chains formed with Arginine 669 and Arginine 358. Output 12 shows an H-bond

side chains formed with Arginine 669.

Induced Fit Docking of 2RIP and Ligand Sugeonol: Output 12 shows an H-bond

backbone formed with –OH group of ligand and Glutamate 205. Output 17 shows two H-bond

side chains formed with –OH group of ligand and Glutamate 206 and Tyrosine 662.

Induced Fit Docking of 2RIP and Ligand Curcumin: Output 1 and 3 show 4 H-bond

side chains between Glutamate 206, Arginine 669, Tyrosine 666 and Tyrosine 585, and a pi-pi

stacking formed between Tyrosine 547 and Phenylalanine 357. Output 5 shows 3 H-bond side

chains between Glutamate 206, Arginine 669 and Tyrosine 666, and a pi-pi stacking formed

between Tyrosine 547 and Phenylalanine 357. Output 10 shows 4 H-bond side chains between

Glutamate 206, Arginine 669, Tyrosine 666 and Tyrosine 547 and a pi-pi stacking formed

between Tyrosine 547 and Phenylalanine 357. Output 11 shows an H-bond side chains

between Tyrosine 547 and an H-bond back bone formed with Arginine 356. Output 14 shows

3 H-bond side chains between Glutamate 206, Arginine 669 and Tyrosine 666. Output 15

shows 5 H-bond side chains between Glutamate 206, Arginine 669, Tyrosine 666, Tyrosine

547 and Tyrosine 585(Glide Score -8.64, Glide Energy -46.33). Output 16 shows 2 H-bond

side chains between Lysine 122 and an H-bond backbone formed with Valine 546.

Induced Fit Docking of 2RIP and Ligand 2, 4- dimethoxy iso flavanone: Output 5

shows 2 H-bond side chains between Tyrosine 547 and Asparginine 71(Glide Score -5.6,

Glide Energy -36.69).


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IFD score is the highest for curcumin: -1625.548084 and second highest for 2, 4-

dimethoxy iso flavanone -1620.206403. Thus curcumin is suggested as the best ligand

and the second best ligand would be 2, 4- dimethoxy iso flavanone.

T – Cell Receptor– CD28 (PDB ID: 1YJD) (Evans, E.J. et al., 2005)

Induced Fit Docking of 1YJD and Ligand alpha cyperone at the Binding Site: C: 201,

C: 202, C: 203: Output 1, 2 and 6show an H-bond backbone formed with Valine 12. Output 7

shows an H-bond side chain between O atom of ligand and Asparginine 19.

Induced Fit Docking of 1YJD and Ligand Cyperene at the binding Site: C:14, C:16,

C:18, C:19, C:8, C:82, C:84. Output 7 and 11 show that the ligand is enclosed by Leucine 11,

Valine 18, alanine 13, Tyrosine 14 and Valine 12, but the site of ligand residue interactions

vary slightly. Output 14 shows that the ligand is enclosed by Asparginine 19, Tyrosine 80, 14,

alanine 17, Valine 18 and Leucine 11.

Induced Fit Docking of 1YJD and Ligand Cyperotundone at the binding Site:

C:99,C:33,C:52,C:57,C:55,C:72,C:30,C:103. Output 1 and 2 show an H-bond formed with

Serine 30. Output 5 shows an H-bond formed with Serine 30 and Arginine 31

Induced Fit Docking of 1YJD and Ligand Kobusone at the binding Site: C:14, C:16,

C:18, C:19, C:8, C:82, C:84. Output 4 shows the ligand enclosed by Asparginine 19, Tyrosine

80, 14 and a water molecule. . Output 5 shows the ligand enclosed by Asparginine 16,

Glutamine 82, Alanine 17, a water molecule and Aspartate 15. Output 7 and 12 show an H-

bond side chain between O atom of the ligand and Asparginine 19. Output 9 shows the ligand

enclosed by Valine 19, Asparginine 19, Tyrosine 14 and Aspartate 15. Output 7 shows an H-

bond side chain between O atom of ligand and Lysine 118.


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Induced Fit Docking of 1YJD and Ligand Sugeonol at the binding Site: C:99, C:33,

C:52, C:57, C:55, C:72, C:30, C:103. Output 1 shows an H-bond back bone formed between –

OH group of ligand and Asparginine 74. Output 4 shows an H-bond back bone formed

between –OH group of ligand Tyrosine 54 and between O atom of ligand and Asparginine 74.

Output 7 shows an H-bond back bone formed between –OH group of ligand Glutamine 56

and between O atom of ligand and Serine 30. Output 9 shows an H-bond back bone formed

between –OH group of ligand and Tyrosine 26 and a side chain with Asparginine 27.

Induced Fit Docking of 1YJD and Ligand curcumin at the binding Site:

C:99,C:33,C:52,C:57,C:55,C:72,C:30,C:103. Output 4 shows an H-bond back bone formed

between –OH group of ligand and Glutamine 56 and Asparginine 53, and a side chain with

Glutamine 57. Output 12 shows 4 H-bond back bones, 2 formed between –OH group of

ligand and Tyrosine 54 and Leucine 58, and 2 formed between O atom of ligand and Arginine

31 and Asparginine 74. Output 20 shows 2 H-bond back bones formed between O atom of

ligand and Asparginine 74 and Serine 30.

Induced Fit Docking of 1YJD and Ligand 2, 4- dimethoxy iso flavanone at the

binding Site: C:99,C:33,C:52,C:57,C:55,C:72,C:30,C:103. Output 2 shows 2 H-bond back

bones formed between O atom of ligand and Asparginine 53 and Serine 30. Output 5 shows

an H-bond back bone formed between O atom of ligand and Asparginine 74. Output 7 shows

an H-bond back bone formed between O atom of ligand and Arginine 31. Output 7 shows an

H-bond back bone formed between O atom of ligand and Serine 30.

Crystal structure of HLA-DM (PDB ID: 2BC4)( Nicholson, M.J. et al., 2006)

Induced Fit Docking of 2BC4 and Ligand alpha cyperone at the binding Site

D:123,D:124,D:125,D:126,D:154,D:179,D:180,D:94,D:95: Output 4 shows an H-bond back


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bone formed between O atom of ligand and Glutamine 39 of chain C, and the ligand is

embedded in the pocked formed by Aspartate 38 and Histidine 16 of chain C, and Proline 124,

Alanine 125 and Tyrosine 156 of chain D. Output 8 shows the ligand is embedded in the

pocked formed by Aspartate 38, 40 and Glutamate 39 of chain C and Glutamate 126 and

Alanine 125 of chain D. Output 4 shows an H-bond back bone formed between O atom of

ligand and Alanine 148 of chain D and the ligand closely bound by Alanine 125, Proline 124,

Tyrosine 123 and 156 of chain D.

Induced Fit Docking of 2BC4 and Ligand Cyperene at the binding Site A:141,

A:142, A:144, A:145, A:146, A:147, A:148, A:150, A:152, A:154, A:156 in order to study the

difference in ligand interaction at a different site. Output 3 shows the ligand is embedded in

the pocked formed by Phenylalanine 149, 44, Glutamine 41, Glycine 32, Serine 151, Proline

29 and Valine 150. Output 10 shows the ligand is embedded in the pocked formed by

Phenylalanine 47, 45, 44, Aspartate 46, Valine 53, 150 and Leucine 33. . Output 15 shows the

ligand is embedded in the pocked formed by Phenylalanine 149, 44, Glutamine 41, Serine

151, 34, Glycine 32, Proline 29 and Valine 150(which is a little similar to output 3).

Induced Fit Docking of 2BC4 and Ligand Cyperotundone at the binding site:

D:123,D:124,D:125,D:126,D:154,D:179,D:180,D:94,D:95: Output 2 shows an H-bond side

chain formed between O atom of ligand and Tyrosine 37 of chain C. Output 3 shows an H-

bond back bone formed between O atom of ligand and Glutamine 39 of chain C. Output 6

shows an H-bond side chain formed between O atom of ligand and Tyrosine 123 of chain D.

Output 9 shows an H-bond back bone formed between O atom of ligand and Alanine 125 of

chain D.


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Induced Fit Docking of 2BC4 and Ligand Kobusone at the binding site:

D:123,D:124,D:125,D:126,D:154,D:179,D:180,D:94,D:95: Output 4, 11 and 12 show an H-

bond back bone formed between O atom of ligand and Glutamine 39 of chain C. Output 5

shows an H-bond back bone formed between O atom of ligand and Alanine 125 of chain D

and an H-bond side chain with Histidine 16 of chain C. Output 6 and 15 show an H-bond back

bone formed between O atom of ligand and Alanine 125 of chain D. Output 7 shows an H-

bond side chain formed between O atom of ligand and Tyrosine 37 of chain C. Output 9

shows an H-bond back bone formed between O atom of ligand and Alanine 125 of chain D.

Induced Fit Docking of 2BC4 and Ligand Sugeonol at the binding site:

D:123,D:124,D:125,D:126,D:154,D:179,D:180,D:94,D:95: Output 6 shows 2 H-bond side

chains with Histidine 16 of chain and C Aspartate 15 of chain D. Output 8 shows H-bond side

chain with Histidine 16 of chain C Threonine 91 of chain D. Output 10 shows 2 H-bond back

bones formed between O atom of ligand and with Glutamine 39 of chain C and Alanine 125

of chain D, and a shows H-bond side chain with Glutamine 126 of chain D. Output 18 shows

H-bond side chain with Aspartate 38 of chain C and H-bond back bones formed between O

atom of ligand and Alanine 125 of chain D.

Induced Fit Docking of 2BC4 and Ligand curcumin at the binding site:

D:123,D:124,D:125,D:126,D:154,D:179,D:180,D:94,D:95 Output 1 shows 2 H-bond back

bones with–OH group of the ligand and Threonine 91 and Alanine 148 of chain D. Output 2

shows 2 H-bond back bones with –OH group of the ligand and Threonine 91 and Alanine 148

of chain D, and an H-bond side chain formed between O atom of ligand and with Tyrosine 37

of Chain C. Output 3 shows an 2 H-bond back bones with Threonine 91 of chain D and –OH

group of the ligand, and between O atom of ligand and with Glutamate 39 of chain C. Output


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4 shows 2 H-bond back bones formed between –OH group of the ligand and Alanine 148 and

Arginine 93 of chain D. Output 5 shows 2 H-bond back bones with–OH group of the ligand

and Threonine 91 and between O atom of ligand and Alanine 125 of chain D. Output 6 shows

2 H-bond back bones with O atom of ligand and Alanine 125 of chain D Glutamate 39 of

chain C. Output 7 shows 2 H-bond back bones with –OH group of the ligand and Arginine 93

and Alanine 148 of chain D. Output 9 shows 3 H-bond back bones with -OH group of the

ligand and Threonine 91, with O atom of ligand and Arginine 93 and Alanine 148 of chain D.

Output 10 shows an H-bond back bone with –OH group of the ligand and Threonine 91, and

an H-bond side chain formed between O atom of ligand and with Tyrosine 37 of Chain C.

Induced Fit Docking of 2BC4 and Ligand 2, 4- dimethoxy iso flavanone at the

binding site: D:123,D:124,D:125,D:126,D:154,D:179,D:180,D:94,D:95. Output 1 and 12

show an H-bond side chain formed between O atom of ligand and with Tyrosine 37 of Chain

C, interactions with other residues do vary. Output 14 shows the ligand embedded in a pocket

bound by Glutamate 126, Alanine 125 and Proline 124 of chain D and Aspartate 38, Histidine

16, Tyrosine 37 and Glutamate 39 of chain C.

The IFD score is the highest for ligand curcumin -1626.591358, which could be

suggested to be the best ligand for this target. The second best ligand is Kobusone, with

an IFD score of -1622.012897, and Glide score of -4.06. . The third best ligand is 2, 4-

dimethoxy iso flavanone, with an IFD score of -1620.781783, a Glide score of-5.6 and

Glide Energy -36.69.

8.1 Conclusion

Most of the docking results for 2, 4- dimethoxy iso flavanone, alphacyperone,

sugeonol, kubsone, cyperotundone and curcumin show significant binding potentials, which is


247

evident from the Induced fit docking score, H bond Score, the Prime Energy and the glide

score. The ligand Cyperene displays the least significant scores for the above parameters

calculated. The best compounds exhibit a pool of inhibitors that would be further tested for

selectivity and cell-based activity, and may serve as starting point for developing inhibitors

for various protein and immune agents related to Type 1 Diabetes that potentially could be

used to treat the autoimmune diseases.

The overall IFD results support that 2, 4- dimethoxy iso flavanone is the best among

the six compounds of Cyperus rotundus which were selected for the docking studies. This

supports the fact that herbal flavonoids have an active role to play in the treatment of the

Autoimmune disease. Curcumin of Curcuma longa has better scores than any of the

compounds of Cyperus rotundus and could be considered as a model compound or a

compound with better binding affinity according to the docking results.

Thus, this research substantiates that, by the modulation of the body immune system

in a beneficial manner, routed through herbal sources such as Cyperus rotundus and Curcuma

longa the T1D autoimmunity could be successfully intervened.

8.2 Cyperus rotundus L. as a potential Break-thourgh for T1D

Of all the compoundsofCyperus rotundus,2, 4- dimethoxy iso flavanone, followed by

sugeonol (8S-hydroxy-1,4R, 9, 9-tetramethyl-3, 4, 5, 6, 7, 8-hexahydro-3a(R), 7-

methanoazulen-2-one) appears to possess the best binding potential as evident from the Glide

score and H bond score. This is followed by kubosone, cyperotundone and alpha cyperone,

while cyperene is shown to possess nil to poor H bond Score.


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Furthermore, earlier animal studies also substantiate the antidiabetic activity of

hydro-ethanolic extract of Cyperus rotundus in alloxan induced diabetes in rats (Raut and

Gaikwad, 2006).

8.3 Immune modulation as a potential treatment for T1D

Of late, many immunotherapies have emerged with a goal to induce autoantigen-

specific tolerance by induction of regulatory T-cells that downregulate immunity to a specific

autoantigen as well as promote tolerance to additional autoantigens (Rewers and Gottlieb,

2009).

Animal studies have shown Cyperus rotundus compounds to possess significant

immune modulatory properties (Aghwan and Al-Taei, 2007)

Curcumin is also is known to possess immune modulatory effect and docking

studies confirm that curcumin to be an effective inhibitor for various protein targets and

immune agents assosciated with T1D.

Thus, the current research is conclusive that immune modulation from herbal

source such as Cyperus rotundus and Curcuma longa could be beneficial to prevent T1D.

8.4 Future perspective

A few other autoantigens that serve as target for various Islet autoantibodies, which

are worth mentioning for further study, but have not been included as part of this study have

been listed below:

1. Islet cell autoantigen 69kD (ICA69), protein product of the human ICA1 gene, is

one target of the immune processes defining the pathogenesis of Type 1 diabetes.


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2. Insulinoma-associated protein 2 : IA-2 (insulinoma-associated protein 2), a major

autoantigen in type 1 diabetes, is a receptor-tyrosine phosphatase-like protein associated with

the membrane of secretory granules of neural and endocrine-specific cells.

3. SOX13: SRY (sex determining region Y)-box 13, also known as SOX13, is a

human gene. This gene encodes a member of the SOX (SRY-related HMG-box) family of

transcription factors involved in the regulation of embryonic development and in the

determination of cell fate. The encoded protein may act as a transcriptional regulator after

forming a protein complex with other proteins. It has also been determined to be a type-1

diabetes autoantigen, also known as islet cell antibody.

4. tyrosine phosphatase IA-2 : autoantigen which is the target of autoantibodies

strongly associated with diabetes development

There is a high possibility that, if this study should lead to a clinical trial the outcome

would be of immense use to the present day diabetic community, because, Once the auto

immunity is arrested, natural multiplication of the existing few beta cells in the system can be

boosted, so that, body produces its own insulin as required to cope with its metabolic

demands.

Defining the interaction between certain T1D autoantigens and the plant compounds

chosen for the study would throw light on how beneficially these can be used and what

outcome could be expected because of their use. The immune modulatory properties of these

compounds are yet to be proved in auto immune diabetics, which, if explored and proved,

would be of immense help to the distressed community that bears the agony of autoimmune

diabetes for a life time.


250

Diabetes affects 246 million people worldwide and, of these, approximately 22

million adults and 0.4 million children have T1D (Aschner, P, et al 2010). Today, a

curative therapeutic approach for the autoimmune diabetic disease is still a dream.

In spite of a multitude of challenges in the field of T1D immunotherapy, there

still remains hope to be realized. Ongoing long-term prospective studies on the field

prove that there still lingers a promise for important insights into disease pathogenesis,

potential avoidable environmental triggers and a possible modulation of the autoimmune

response towards a longstanding or even a permanent restoration (Subha, K. et al 2008).

Better understanding of the role of single antigens during disease progression and

response to therapy, by targeting cytokines/chemokines, NK-T-cells, adhesion

molecules, APCs and T-cells would be helpful. Various trials in recent-onset T1D that

explore antigen-specific/non-specific, β-cell regeneration/replication possibilities and

prevention trials (like the anti-CD3 trials) that dig in search of systemic immune

modulators are in progress. Tracking induced Treg responses to monitor trial would also

be of worth(Maria K., et al. 2008).


Documents

8.0 Discussion and conclusion 1965shodhganga.inflibnet.ac.in/.../43802/11/11_chapter8.pdf · 2018-07-03 · 8.0 Discussion and conclusion In the Type 1 diabetes or autoimmune diabetes,