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In silico Molecular Docking and ADME/T Analysis of Some Selected Isolated Compounds of Phyllanthus emblica against Type 2 Diabetics

Jackie B1, Sagar S2, Alamgir H3, Razowanul Md F4, Sumaiya F2, Emon D2, Hasan Md4, Arafat F5, Mohammed F5, and Ramjan Ali Md4*

1Comilla Medical College, Faculty of Medicine, University of Chittagong, Bangladesh

2Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh

3Department of Chemistry, Jahangirnagar University, Savar, Dhaka, Bangladesh

4Department of Pharmacy, Jagannath University, Dhaka, Bangladesh

5Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh

*Corresponding Author:
Md. Ramjan Ali
Department of Pharmacy, Jagannath University
Dhaka, Bangladesh
Tel: +8801766040786
E-mail: [email protected]

Received Date: September 26, 2018; Accepted Date: October 17, 2018; Published Date: October 22, 2018

Citation: Jackie B, Sagar S, Alamgir H, Razowanul Md F, Sumaiya F, et al. (2018) In silico Molecular Docking and ADME/T Analysis of Some Selected Isolated Compounds of Phyllanthus emblica against Type 2 Diabetics. Am J Ethnomed Vol.5 No.2:9

DOI: 10.21767/2348-9502.10009

 
Visit for more related articles at American Journal of Ethnomedicine

Abstract

The aim of this study is to perform sub-atomic docking scores to recognize potential binding affinities of the phytochemicals from Phyllanthus emblica. Successful disclosure of against diabetic agent has been contributed by computer based drug design approach. Molecular docking and ADME/T analysis continue being an extraordinary guarantee in the field of computer based drug design. An extensive variety of docking score found by molecular docking and Swiss ADME used for ADME/T analysis to select a potent drug compound.

Keywords

Phyllanthus emblica; Molecular docking; ADME/T analysis; Type 2 diabetics; Kaempferol

Introduction

Diabetes, regularly referred to by specialists as diabetes mellitus, depicts a gathering of metabolic sicknesses in which the individual has high blood (glucose), either on the grounds that insulin generation is deficient, or on the grounds that the body's cells don't react legitimately to insulin, or both [1,2]. It is assessed that in 2010 there were internationally 285 million individuals (roughly 6.4% of the grown-up population) experiencing this disease. This number is assessed to increment to 430 million without better control or cure [1,3,4]. Diabetes has become an intense medical issue with a substantial financial weight to every nation. With regards to the general ascent of diabetics around the world, a more quick development is found in the Asian regions. The top five Asian countries are: India (50.8 million), China (43.2 million), Pakistan (7.1 million), Japan (7.1 million) and Indonesia (7 million). Bangladesh is expected to replace Japan in 2030 and rank at the 8th [5,6].

Phyllanthus emblica is a species of flowering plant of the genus Phyllanthus in the Phyllanthaceae family. It is planted through the deciduous of tropical India, Uttar Pradesh, Tamil Nadu, Rajasthan and Madhya Pradesh. The tree is little to medium in estimate, achieving 1-8 m (3 ft 3 in to 26 ft 3 in) in stature. The branchlets are not glabrous or finely pubescent, 10-20 cm (3.9-7.9 in) long, typically deciduous; the leaves are straightforward, subsessile and firmly set along branchlets, light green, looking like pinnate clears out. The flowers are greenish-yellow. The fruit is about round, light greenish yellow, very smooth and hard on appearance, with six vertical stripes or wrinkles [7-11]. The fruit, seed, leaves, root, bark and flowers are used in various Ayurvedic or Unani herbal preparations. It might be utilized as a rasayana to advance life span, and customarily to improve assimilation, treat constipation, lessen fever, sanitize the blood, decrease cough, mitigate asthma, reinforce the heart, advantage the eyes, fortify hair development, breathe life into the body, and upgrade intellect [11,12].

Molecular docking is a fundamental instrument in the difference in new remedies. Docking method stipends depicting the direct of a test little particle in the coupling site of the receptor target of interest. A profitable docking procedure must be able to satisfactorily imagine the nearby ligand speak to the receptor constraining site (i.e.to discover the preliminary ligand geometry inside a specific obstruction limit) and the related physicalcompound sub-molecular affiliations [13,14].

The aim of study to discover a novel compounds against diabetics and ADME/T property studies used to measure the safety of the compounds as drug.

Methods and Materials

Preparation of protein

From Protein Information Bank 3D crystal structure of Pancreatic Alpha-Amylase With A carbohydrate Inhibitor (PDB 1PPI) is downloaded [15,16]. By utilizing the Protein Readiness Wizard of Schrödinger-Maestro v 10.1 the structure was arranged and refined. Charges furthermore, bond orders were doled out, hydrogens are added to the overwhelming iotas, were changed over to methionines, and all waters were erased. By Utilizing power field OPLS_2005 minimization was completed setting greatest overwhelming molecule RMSD to 0.30 Å.

Preparation of ligand

Compounds were reprocessed from PubChem databases i.e 1,1-diphenyl-2-picrylhydrazyl (CID 2735032), isocorilagin (CID 10077799), kaempferol (CID 5280863), kaempferol 3-bita-Dglucopyranoside (CID 5318761) and quercetin (CID 5280343)

Receptor grid preparation

Receptor matrices were computed for arranged proteins to such an extent that different ligand presents tie inside the anticipated active site during docking. Grids were created keeping the default parameters of van der Waals scaling factor 1.00 and charge cutoff 0.25 subjected to OPLS 2005 power field in glide. A cubic box of particular measurements revolved around the centroid of the active site buildups (Reference ligand active site) was created for receptor. For docking tests, The bouncing box was set to 14 × 14 × 14 [17,18].

Glide standard precision (SP) ligand docking

SP adaptable ligand docking was completed in glide of Schrödinger- Maestro v10.1, inside which penalties were connected to non-cis/ trans amide bonds. Vanderwaals scaling component and fractional charge cutoff was chosen to be 0.80 and 0.15, respectively for ligand atoms. Final scoring was performed on energy minimized postures and showed as glide score. The least glide score esteem was recorded for every ligand as the best docked present.

Ligand based ADME/Toxicity prediction

The QikProp module of Schrodinger (Maestro, version 10.1) is a quick, accurate, easy-to-use absorption, distribution, metabolism, and excretion (ADME) prediction program design to produce certain descriptors related to ADME. It predicts both physicochemical significant descriptors and pharmacokinetically relevant properties. ADME properties determine drug-like activity of ligand molecules based on Lipinski’s rule of five. ADME/T properties of the compound (DIM) was analyzed using Qikprop 3.2 module [19,20].

Result

In silico molecular docking analysis

In order to study the interaction of the compounds 1,1-diphenyl- 2-picrylhydrazyl (CID 2735032), isocorilagin (CID 10077799), kaempferol (CID 5280863), kaempferol 3-bita-D-glucopyranoside (CID 5318761) and quercetin (CID 5280343) with 1PPI, we performed Glide docking analysis by Schrodinger suite v10.1, where among of these compounds kaempferol shows highest docking score shown in Table 1. The negative and low value of free energy of binding demonstrates a strongly favorable bond between 1PPI and kaempferol in most favourable conformations.

Table 1: Docking results of 1,1-diphenyl-2-picrylhydrazyl (CID 2735032), isocorilagin (CID 10077799), kaempferol (CID 5280863), kaempferol 3-bita-D-glucopyranoside (CID 5318761) and quercetin (CID 5280343) with α-amylase enzyme (PDB: 1PPI).

Compound Name Compound ID Docking Score
Quercetin 5280343 -7.58
Kaempferol 5280863 -7.706
Kaempferol 3-bita-D-glucopyranoside 5318761 -6.313
Isocorilagin 10077799 -5.67
1,1-Diphenyl-2-picrylhydrazyl 2735032 -3.088

Discussion

The aim of molecular docking is the accurate prediction of the structure of a ligand within the constraints of a receptor binding site and to correctly estimate the strength of binding. The binding mode of Pancreatic Alpha-Amylase with A carbohydrate Inhibitor (PDB 1PPI) was investigated by doing computational analysis, glide docking. Both glide standard (SP) had been introduced. The results of docking analysis were described in Table 1 and the docking figure showed in Figure 1. Among all the compounds kaempferol showed the well docking score. Because the negative and low value of free energy of binding demonstrates a strongly favorable bond is preferable for best docking study. So the docking score between 1PPI and kaempferol in most favorable conformations.

ethnomedicine-interactions

Figure 1: 2D representation of the interactions between the best pose found for quercetin (A), kaempferol (B), kaempferol 3-bita-Dglucopyranoside (C), isocorilagin (D) and 1,1-diphenyl-2-picrylhydrazyl (E) with α-amylase enzyme (PDB: 1PPI).

ADME/T analysis shown in Table 2, the selected properties are known to influence metabolism, cell permeation, and bioavailability. Predicted properties of isocorilagin and kaempferol 3-bita-D-glucopyranoside were not within the range for satisfying all the Lipinski’s rule of five to be considered as drug like potential. But on the other hand kaempferol was satisfying all the Lipinski’s rule of five to be considered as drug like potential (Figure 2).

Table 2: ADME/T properties 1,1-diphenyl-2-picrylhydrazyl (CID 2735032), isocorilagin (CID 10077799), kaempferol (CID 5280863), kaempferol 3-bita-D-glucopyranoside (CID 5318761) and quercetin (CID 5280343) by SwissADME.

Name of molecule MWa HB donorb HB acceptorc Log Pd Molar refractivitye
Quercetin 302.24 g/mol 5 7 1.23 78.03
Kaempferol 286.24 g/mol 4 6 1.58 76.01
Kaempferol 3-bita-D-glucopyranoside 594.52 g/mol 9 15 -1.2 139.36
Isocorilagin 634.45 g/mol 11 18 -0.71 141.85
1,1-Diphenyl-2-picrylhydrazyl 394.32 g/mol 0 7 1.36 109.73
ethnomedicine-quercetin

Figure 2: Best ranked pose of quercetin (A), kaempferol (B), kaempferol 3-bita-Dglucopyranoside (C), isocorilagin (D) and 1,1-diphenyl-2-picrylhydrazyl (E) in the binding pocket of α-amylase enzyme (PDB: 1PPI).

Conclusion

From the study it was found that, Nauclea latifolia could be great source of new α-amylase inhibitor. In silico model support that all the isolated compounds from N. latifolia might be α-amylase inhibitor. Among all the compounds kaempferol showed well docking score.

Acknowledgement

The authors express gratitude toward GUSTO A Research Group for giving the financial support and software.

References

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