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Anticancer potential of isolated phytochemicals

from Ocimum sanctum against breast cancer: In
silico Molecular docking...
Poster December 2016
DOI: 10.13140/RG.2.2.20939.18725

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Anticancer potential of isolated phytochemicals from Ocimum sanctum

against breast cancer: In silico Molecular docking approach
Arkajyoti Paula,b, Mohammad Shah Hafez Kabira,c*, Mir Muhammad Nasir Uddina,d, Md. Mominur
Rahmana,c, Abul Hasanata,c, Tanvir Ahmad Chowdhurya,c, Md. Nazim Uddin Chya,c, Md. Rakibul Hasana,c
aGUSTO A Research Group, Chittagong-4000, Bangladesh, bDepartment of Pharmacy, BGC Trust University Bangladesh,
Chittagong-4000, Bangladesh, cDepartment of Pharmacy, International Islamic University Chittagong, Chittagong-4318,
Bangladesh, dDepartment of Pharmacy, University of Chittagong, Chittagong-4331, Bangladesh

Abstract

RESULTS

Breast cancer is an increasing public health problem. One of the

main causes of breast cancer is estrogen receptor alpha. Over
expression of estrogen receptor is seen in number of cases of
breast cancer. The aim of this study was to screen out the
effective bioactive compounds from Ocimum sanctum namely
Carvacrol, Palmitic Acid, Stearic Acid, Vicenin, which may be
potential inhibitors of estrogen receptor alpha (ER-) for searching a
drug against the breast cancer. A wide range of docking score found
during molecular docking by Schrodinger. Carvacrol, Palmitic Acid,
Stearic Acid, Vicenin showed the docking score -6.456, 2.232, 1.985
and -2.941 respectively. Among all the compounds Carvacrol showed
best docking score towards estrogen receptor alpha. So, Carvacrol is
the best compounds for selective inhibitors of estrogen receptor alpha,
as it possessed best value in Molecular docking. Further in vitro and in
vivo investigation need to identify estrogen receptor alpha inhibitory
activity of isolated compounds from Ocimum sanctum.
Keywords: Ocimum sanctum, estrogen receptor alpha, Breast cancer,
Carvacrol.

Table 1: Docking results of Carvacrol, Palmitic Acid, Stearic Acid,

Vicenin with estrogen receptor alpha (PDB: 3ERT).
Compound Name

Docking Score

Carvacrol

-6.456

Palmitic Acid

2.232

Stearic Acid

1.985

Vicenin

-2.941

MATERIALS AND METHODS

Protein Preparation
Three-dimensional crystal Structure of estrogen receptor alpha (PDB
id: 3ERT) was downloaded in pdb format from the protein data bank.
After that, the structure was prepared and refined using the Protein
Preparation Wizard of Schrdinger-Maestro v10.1. Charges and bond
orders were assigned, hydrogens were added to the heavy atoms,
selenomethionines were converted to methionines, and all waters were
deleted. Using force field OPLS_2005, minimization was carried out
setting maximum heavy atom RMSD (root-mean-square-deviation) to
0.30 .
Ligand Preparation
Compounds were retrieved from PubChem databases, i.e. Carvacrol,
Palmitic acid, Stearic acid, and Vicenin.
Glide Standard Precision (SP) ligand docking
SP flexible ligand docking was carried out in Glide of SchrdingerMaestro v 10.1 within which penalties were applied to non-cis/trans
amide bonds. Van der Waals scaling factor and partial charge cutoff
were selected to be 0.80 and 0.15, respectively for ligand atoms. Final
scoring was performed on energy-minimized poses and displayed as
Glide score. The best-docked pose with lowest Glide score value was
recorded for each ligand.
Ligand based ADME/Toxicity prediction
This analysis is done by following server,
http://www.scfbioiitd.res.in/software/drugdesign/lipinski.jsp#anchort
ag
https://ilab.acdlabs.com/iLab2/index.php
http://www.molinspiration.com/cgi-bin/properties

RESEARCH POSTER PRESENTATION DESIGN 2015

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Figure 1: Docking results of A. Carvacrol, B. Palmitic Acid, C. Stearic Acid,

D. Vicenin with estrogen receptor alpha (PDB: 3ERT).
Table 2: ADME/T Properties of Palmitic acid, Carvacrol, Stearic acid,
Vicenin.
Name of
molecules
Palmitic acid

MW

HB donor

HB acceptor

Log P

241

3.245709

Molar
Refractivity
61.196991
52.472488

Carvacrol

154

2.845099

Stearic acid

267

3.789889

68.513985

Vicenin

594

14

6.241352

157.647232

Molecular

mass less than 500 Dalton

than 5 hydrogen bond donors
Less than 10 hydrogen bond acceptors
High lipophilicity (expressed as LogP less than 5)
Molar refractivity should be between 40-130
Less

CONCLUSION
Among all the compounds Carvacrol showed best docking score
towards estrogen receptor alpha. So, Carvacrol is the best compounds
for selective inhibitors of estrogen receptor alpha, as it possessed best
value in Molecular docking. Further in vitro and in vivo investigation
need to identify estrogen receptor alpha inhibitory activity of isolated
compounds from Ocimum sanctum.

REFERENCES
Ahmed B, Ashfaq UA, ul Qamar MT, Ahmad M: Anticancer potential of phytochemicals
against breast cancer: Molecular docking and simulation approach. Bangladesh Journal
of Pharmacology 2014, 9(4):545-550.
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll
EH, Shelley M, Perry JK: Glide: a new approach for rapid, accurate docking and scoring.
1. Method and assessment of docking accuracy. Journal of medicinal chemistry 2004,
47(7):1739-1749.
Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin
PC, Mainz DT: Extra precision glide: docking and scoring incorporating a model of
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