Insilico Prediction of Binding Efficiency for the Phytoconstituents from Traditional Medicinal Plants against Diabetes Target: Aldose Reductase

 

R. Sathish Kumar1*, C. Aarthi2

1Assistant Professor, Department of Botany, PSG College of Arts and Science, Coimbatore.

2Department of Biochemistry, PSG College of Arts and Science, Coimbatore.

*Corresponding Author E-mail: sathishbioinf@gmail.com

 

ABSTRACT:

Diabetes mellitus is a most common metabolic disease arising from lack of insulin production or insulin resistance. Diabetes mellitus is a leading cause of morbidity and mortality. Aldose reductase, a clinically important key enzyme which is involved in the polyol pathway and considered as the main factor for the pathogenesis of many diabetic complications. The aim of the present study is to combat and manage the diabetic mellitus using traditional medicinal plants. The phytoconstituents which are biologically active in plants Silybummarianum (milk thistle), Abelmoschusesculentus (okra), Allium cepa (onion), Withania somnifera (winter cherry), Commiphora wightii (Guggul), Eriobotrya japonica (loquat) and Cinnamomum verum (cinnamon) were identified from the literature and the 3D structure were retrieved from the publicly accessible chemical compound, PubChem. The compounds were docked with the target aldose reductase using glide module of Schrodinger software. Among the 120 number of compounds, taxifolin from Silybummari anum showed least G score value of -11.11 Kcal/mol. The compound taxifolin had significantly interacted with 5HA7 protein and further information are discussed in detail.

 

KEYWORDS: Diabetes mellitus, Medicinal plants, PubChem, docking studies, taxifolin.

 


INTRODUCTION:

Diabetes mellitus is a most common metabolic disease and exist as a leading cause of morbidity and mortality. Over 171million people worldwide are affected with diabetes mellitus in 2000 and the incidence is expected to grow steadily to 366 million by 20301.Diabetes is pandemic in both developed and developing countries. In India alone, diabetes is expected to increase from 40.6 million in 2006 to 79.4 million by 2030.Studies have shown that the prevalence of diabetes in urban Indian adults is about 12.1%2. The most common complications prevail among diabetic patients are neuropathy, nephropathy, retinopathy, cataracts and even stroke.

 

These complications are expected to arise from chronic hyperglycemia, which damages the blood vessels and peripheral nerves. Primarily, the hyperacivity of polyol metabolic pathway results in accumulation of cellular sorbitol which further imposesosmotic stress on cell sandimply microvascular damage to retina, kidney as well as nerve system. The increased formation of advanced glycation end products (AGEs) is the second reason to be considered since it activates the nonenzymatic glycosylation of proteins and lipids, which leads to dysfunctional behaviors of related enzymes and receptors. The third is hyperglycemia-induced activation of protein kinase C (PKC) isoforms leads to pathological changes in growth factor expression. The excess intracellular glucose into the hexosamine pathway, unconditional modification of enzymatic proteins by N-acetylglucosamine along with abnormal enzyme behaviors are some of the other factors responsible for diabetic situation. Finally, it was proposed that hyperglycemia-induced impairment of antioxidant defense such as the overproduction of reactive oxygen species (ROS) readily initiates inflammation responses in the patients3. Under normal circumstances, in mammalian cells, the cellular glucose is predominantly phosphorylated into glucose 6-phosphate by hexokinase and enters the glycolytic pathway, only trace amounts of non-phosphorylated glucose (about 3%) enter the polyol pathway4. However, under hyperglycemic condition, increased flux through the polyol pathway which accounts for greater glucose metabolism5,6.The protein aldose reductase (AR) acts as catalyze as well as rate limiting step of the polyol pathway in reducing glucose to sorbito lAR has been isolated and purified from human and animal tissues including various regions of the eyes7, testis8, liver9, placenta10,11 ovary12 kidney13,14, erythrocyte15, cardiac11 and skeletal muscle16,17,11, and the brain18,19. Flynn has stated that AR is located in the cytoplasm of most cells; however, distribution varies in cell types of each organ20.

 

Throughout the world, 4,22,000 flowering plants are reported for existence, in that more than 50,000 are utilized for medicinal purpose21. Especially in India, about 43% of the total flowering plants are of medicinal importance. Moreover, in developing countries, 80% of the human population have already started relying on plant resources for healthcare purpose. Milk thistle (Silybummarianum) belongs to Asteraceae family, has been reported to be used as an herbal remedy for a variety of ailments, particularly liver, kidney, and gall bladder problems, has unique ability to protect the liver for the past 2,000 years.

 

The plant Allium sepa was reported for its anti-diabetic effects on alloxan-induced diabetic Rattus novergicus22. A. sepa is called as onion, which is common in the preparation of food in India. The bulb is reported for anthelmintic, anti-inflammatory, antiseptic, antispasmodic, carminative, diuretic, expectorant, febrifuge, hypoglycemic, hypotensive, lithotripsic, stomachic and tonic23. Moreover, the functional food are mentioned as effective on diabetes24, Cinnamomumverum is used as a spice/herb also received wide acceptance as an important ingredient in food and traditional medicine. The plant has already been studied for its efficiency in inhibiting the enzymes α-amylase and α-glucosidase, where these enzymes are known for its role in managing the type-2 diabetes25. The hypoglycemic activity of Eriobotrya japonica seeds were reported in type 2 diabetic rats and mice26. The plant Abelmoschusesculentusis also medicinally important for diabetic conditions. Therefore, the biologically active molecules from the above mentioned plants are to be focused in the present study for its efficient binding property as well as inhibitory effect of aldose reductase (AR) has to be achieved through docking analysis.

 

MATERIALS AND METHODS:

The 3D structure of protein Aldose reductase(AR) was retrieved from Protein Data Bank (www.rcsb.org) of ID: 5HA7. The 3D structures of plant compounds were retrieved from PubChem database, a small molecule resource. The plant compounds are taxifolin, eriodyctiol, dihydro-kaempferol, kaempferol, hispid one, protocatechuic acid-4-glucoside, 3-hydroxy flavones, eugenol oxide, dehydro-1, 8-cineole, D xylose, eucalyptol, myrecene epoxide, chlorogenic acid, cinnamaldehyde and pectin. The active site for AR was predicted using an online tool Lignite (http://projects.biotec.tu-dresden.de/pocket/). The ADMET properties for the ligands were determined using Qik prop module and the docking analysis was carried out in Glide module of Schrodinger software. The results of target-ligand interactions were observed using PyMol viewer.

 

RESULT AND DISCUSSION:

The energetically favorable binding sites of the protein was predicted using Ligsite tool which based on the interaction energy and a simple Vander Waals force, the binding sites are clustered and ranked according to their spatial proximity and sum of interaction. The determine active site residues are SER2, PRO13, ILE14, LEU15, TRP20,LYS21,GLY38,GLN192,SER210,SER214,ASP216,ARG217,PHE273,PHE276,ASN294,ARG296,GLU314 and PHE315.The result of docking analysis was tabulated (Table 1) showing the G. score, interacting residues, number of hydrogen bonds and bond length. Taxifolin had least G.score of -11.11 Kcal/mol and significant interactions were observed with residues located at their active site pocket. The residues like ASN160 andVAL47 are involved in the hydrogen bond formation of bond length 2.0 and 1.7 Å. The interaction of receptor with taxifolin was shown (Fig.1). Among the active site residues predicted, the polar uncharged amino acid SER (S) and hydrophobic amino acid TRP (W) were identified to form hydrogen bonds with the plant compounds protocatechuic acid 4-glucoside, D-xylose and pectin. Apart from these two, the residues THR19, ASP43, TYR48, TRP111, ASN160, GLN183 and LEU300 are mostly involved in forming hydrogen bonds. The compound protocatechuic acid 4-glucoside, D-xylose and pectin had G.score of -9.59, -6.85 and -7.83 Kcal/mol. Though these compounds were observed with less G.score than taxifolin (-11.11 Kcal/mol), the hydrogen bond interactions were observed with the predicted active site residues of the receptor. The bond length of taxifolin was between 1.5 to 2.2 Å, which indicated its moderate strength of the bonds, whereas the residue TRP20 showed 1.9Å of bond length with both protocatechuic acid 4-glucoside and D-xylose. SER210 formed single hydrogen bond with protocatechuic acid 4-glucoside and D-xylose and had two interactions in the case of pectin. The bond length were observed to be in the range of 2.2-2.7Å. The compounds like eriodyctiol, dihydrokaempferol and hispidone had G.score of -10.5, -10.07 and -10.31 Kcal/mol. The plant compounds were observed to show G.score in the range -6 to -11 Kcal/mol, in which the higher G.score (-6 Kcal/mol) were observed with the compounds dehydro-1,8-cineole, D-xylose, eucalyptol, myrcene epoxide and cinnamaldehyde. The compound pectin of Abelmoschusesculentus plant had -7.83 Kcal/mol of G. Score and had maximum number of hydrogen bonds when compared to other compounds studied in the present analysis. The interactions were observed with ASP43, ILE260, SER210 and TYR48. Eugenol oxide of Allium cepa also had -7.78 Kcal/mol, whereas 3-hydroxy flavone of the same plant, alone had G.score of -8.42 Kcal/mol, however, the single interaction only observed with 3-hydroxy flavone.

Moreover, the ADME toxicity properties was analysed only for taxifolin satisfactorily obeyed the Lipinski rule of 5. Diabetes, being a common and most prevailing disease among majority of the population throughout the world, the necessary measures has to be taken in order to overcome the existing problem posed by the diabetes. The compounds from spice plants like Zingiberofficinale, Curcuma longa, Allium sativum and Trigonellafoenum were analyzed for its efficient binding with AR, which described the gingerinones A, B and C, lariciresinol, quercetin and calebin A had least docking score and observed with sustained protein-ligand interactions27. Similarly, in the present study also, the compounds protocatechuic acid and D-xylose had scored better than the other plants selected here. This clearly indicates the efficiency of functional foods to exhibit significant activity against type 2 diabetes24. Further, the study would be carried for molecular dynamics to analyze the stability of the protein-ligand complex.


 

Table 1: Interactions of Plant compounds with Aldosereductase


S.No

Ligand Name (PubChem ID)

Residues Interaction

Bond Length (Å)

No. of Hydrogen Bonds

G-Score (Kcal/mol)

Silybummarianum

1

Taxifolin (442540)

ASN160 (O-H)

VAL47 (H-O)

2.0

1.7

2

-11.11

2

Eriodyctiol (440735)

ASN160 (O-H)

GLN183 (H-O)

1.7

1.5

2

-10.5

3

Dihydrokaempferol (14254854)

ASP43 (H-O)

GLN183 (H-O)

TRP111 (O-H)

LEU300 (O-H)

2.3

1.7

2.5

2.5

4

-10.07

4

Keampferol (5280633)

TRP111 (O-H)

GLN183 (H-O)

2.8

2.5

2

-9.79

Allium cepa

5

Hispidone (9997719)

ASN160 (O-H)

GLN183 (H-O)

1.7

1.5

2

-10.31

6

Proto catechuic acid 4-glucoside (91309592)

ASP43 (H-O)

THR19 (O-H)

TRP20 (O-H)

SER210 (O-H)

1.7

2.4

1.9

2.2

4

-9.59

7

3-hydroxy flavone (11349)

ASN160 (O-H)

2.3

1

-8.42

8

Eugenol oxide  (92349)

TYR48 (O-H)

1.9

1

-7.78

9

Dehydro-1,8-cineole (11228907)

ASN160 (O-H)

2.3

1

-6.9

10

D-xylose (135191)

SER210 (O-H)

ASP43 (H-O)

THR19 (O-H)

TRP20 (O-H)

2.4

2.0

2.9

1.9

4

-6.85

11

Eucalyptol (2758)

ASN160 (O-H)

2.5

1

-6.52

12

Myrcene epoxide  (122371)

TYR48 (O-H)

1.8

1

-6.50

Eriobotrya  japonica

13

Chlorogenic acid (1794427)

TRP111 (O-H)

GLN183 (H-O)

2.8

2.5

2

-9.79

Cinnamomum verum

14

Cinnamaldehyde (637511)

TYR48 (O-H)

2.0

1

-6.90

Abelmoschusesculentus

15

Pectin (441476)

ASP43 (H-O)

ILE260 (H-O)

SER210 (O-H)

TYR48 (O-H)

SER210 (O-H)

2.6

1.8

2.4

2.0

2.7

5

-7.83


Fig. 1: Interaction of taxifolin with Aldose Reductase

 

CONCLUSION:

The present study indicated the efficiency of plant compounds in inhibiting the aldose reductase (AR) enzyme, where the least G.score was observed with taxifolin. Apart from taxifolin, the compounds like protocatechuic acid 4-glucoside, D-xylose and pectin were also signify its efficacy against AR by the formation of hydrogen bond interactions with the active site residues predicted using the online tool. Henceforth, the study in future focuses on determining the stability of the interactions observed with the above mentioned compounds.

 

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Received on 01.08.2017          Modified on 16.08.2017

Accepted on 21.08.2017        © RJPT All right reserved

Research J. Pharm. and Tech 2017; 10(11): 3709-3712.

DOI: 10.5958/0974-360X.2017.00673.4