world journal of pharmaceutical research swechha et al

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Swechha et al. World Journal of Pharmaceutical Research

IN-SILICO STUDY OF GERANIOL ANALOGS AGAINST EGFR FOR

VALIDATING ITS POTENCY TO BE CANDIDATE CANCER DRUG

Swechha Mishra*

Indian Institute of Information Technology, Allahabad, India.

ABSTRACT

Receptor tyrosine kinase is a key regulator of various physiological

pathways. Anomaly in this protein might lead to cancer, and therefore

it holds great potential to be potent target for combating cancer .With

the aim of validating effect of geraniol analogs on tyrosine kinase, in-

silico screening was carried out. In this study we have taken different

geraniol derivatives and performed molecular docking against receptor

tyrosine kinase in order to check the efficiency of docking. Further

toxicity test was performed to detect the compatibility of selected

compound to that with the human system.

KEY WORDS: Geraniol, EGFR, Auto dock, Docking.

1) INTRODUCTION

Uncontrolled growth of cell in tissues of the lung can be characterized as cancer of lungs or

in general, carcinoma of lung. One of the prominent characters of lung cancer is coughing up

blood [1].The epidermal growth factor receptor (EGFR) is one of the regulatory factors for

various physiological functions. EGFR is one of the major targets for the treatment of lung

cancer, and mutation of EGFR is commonly seen in non-small-cell lung cancer. There are

various other genes also that undergo mutation very oftenly like PIK3CA, LKB1, BRAF [2]

over expression of receptors of the erbB family including the epidermal growth factor

receptor (EGFR) encoded by erbB-1 leads to the Non-small-cell lung cancer. The EGFR is a

type of receptor tyrosine kinases (TK) that weighs 170 kilodaltons .When several specific

ligands binds, It phosphorylates and dimerizes [3]. Mutation in these tyrosine kinases lead to

constitutive expression that may results to cancer. There is need to develop better methods

that could be more effective and have significantly less side effects [4].

World Journal of Pharmaceutical ReseaRch SJIF Impact Factor 5.045

Volume 3, Issue 6, 1444-1453. Research Article ISSN 2277 – 7105

Article Received on 20 June 2014, Revised on 15 July 2014, Accepted on 10 August 2014

*Correspondence for

Author

Swechha Mishra

Indian Institute of Information

Technology, Allahabad, India..


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Studies have shown that monoterpenes exert antitumor activities and suggested that these

components are a new class of cancer chemopreventive [5]. Geraniol, an acyclic monoterpene

alcohol found in lemongrass and aromatic herb oils, has been shown to exert in vitro and in

vivo antitumor activity against murine leukemia, hepatoma, and melanoma cells (6). It has

been found from Previous in vivo tumor model that geraniol exerted chemotherapeutic or

chemosensitizing activity against several types of cancers, including colon, pancreatic,

hepatic, and prostate cancer( 7 -10) Mechanisms of anticancer action of geraniol are not well

understood but it might involve the mevalonate metabolism by inhibiting HMG-CoA

reductase activity ( 11 ), In addition, although certain types of monoterpenes, such as menthol,

linalool, and cineol, are structurally and functionally similar to geraniol ( 12), the specificity of

therapeutic actions of geraniol are only slightly evaluated. In our current studies we are

taking up different geraniol derivatives and performing docking studies against receptor

tyrosine kinase. The one showing minimum docking energy has been chosen for further

studies of toxicity.

2) METHODS AND MATERIALS

2.1. Target Selection

Target for computational analysis of binding energies was retrieved via protein data bank

(PDB (ID: 1M17)

2.2 Active site prediction [13]

Cast-p was used for the prediction of active site of the protein

2.3. Ligand Screening

Primary ligand screening was done on the basis of Lipinski rule of 5.Out of 200 compounds

19 were taken after screening. These 19 compounds were further screened on the basis of

number of rings present. After secondary screening 7 compounds were selected for the

further procedure.

2.4. Molecular Docking

Docking studies were performed in rigid parameters. To get a functionality of the protein, its

3D structure is required. The 3D structure of EFGR tyrosine kinase domain was retrieved

from RCSB .since far the best known method that is known today for predicting the activity

of ligand and protein is docking. Now a days it’s being one of the prominent technique to

predict protein –ligand interactions .Natural ligands that were selected through literature


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search and docked with the protein 3D structure which was retrieved from RCSB .Auto

Dock 4.2 [ 14] was used for virtual screening .Protein has gone through with Docking

calculation. Salvation parameters, Kollman charges, and hydrogen atoms were added. In case

of the ligands non-polar hydrogen atoms were merged and rotatable bonds were defined

gasteiger partial charges were added to the ligands. Torsions were defined. Spacing and

affinity (grid) map of 60 × 60 × 60 angstrom were generated. Lamarckian genetics algorithm

was used for performing Docking simulation .Ten different runs were generated for each

experiment, and all the selected ligands were gone through this process.

2.5. Toxicity prediction

Toxicity of various ligands was predicted with open tox [15].

3) RESULTS AND DISCUSSION

Secondary Screening

7 compounds were screened on the basis of no. of ring structures which should be less than 4.

TABLE 1: SECONDARY SCREENING RESULT

S.No. STRUCTURE COPOUND NAME COMPOUND ID RINGS

1

p-Dimethylaminoazobenzene 6053 2

2

o-Aminoazotoluene 7340 2

3

4-amino-3-chlorobenzoic acid 17211 1

4

Neryl alcohol 643820 0

5 Geranyl formate 5282109 0


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6

Geranyl ethyl ether 5356487 0

7

8-Hydroxy geraniol 6430784 0

Inference: 7 ligands were screened out on the basis of no. of rings present in the structure. Table 2: Docking Result Of Ligands

Table 3: Docking Result of Drugs

Table 4: Comparative Toxicity Of Best Drug And Ligand

Results of final screening is in table 1, Docking results has been summoned up in table 2 and

table 3 respectively. Binding result calculation and interaction between receptor and ligand is

explained in it. All the ligands were docked in an active pocket of the receptor. As in Table 1

S.No Scientific name Ligand Id Binding

energy Gb (kcal/mol)

Intermolecular energy

Torsional energy

Internal energy

Inhibition constant

1 p-Dimethylaminoazobenzene 6053 -5.54 -6.44 .89 -.44 86.85 2 o-Aminoazotoluene 7340 -6.02 -6.91 .89 .29 38.73 3 4-amino-3-chlorobenzoic acid 17211 -4.73 -5.63 .89 .03 339.67 4 Neryl alcohol 643820 -4.63 -6.12 1.49 -.41 406.81 5 Neryl alcohol 5282109 -4.41 -6.2 1.79 -0.33 588.08 6 Geranyl ethyl ether 5356487 -4.69 -5.29 0.6 -0.06 364.79 7 8-Hydroxy geraniol 6430784 -4.49 -6.88 2.39 -.48 509.79

S.NO Compound id

Binding energy, Gb (kcal/mol)

Intermolecular energy

Torsional energy

Internal energy

Inhibition constant

1 123631 -6.15 -8.54 2.39 -0.81 3.91 2 208908 -6.83 -10.11 3.29 -1.1 9.84 3 3062316 -5.83 -8.21 2.39 -0.66 53.64 4 5291 -7.47 -9.26 1.79 -0.17 3.33

NAME ID xLogP Environmental fate parameter

Ecotoxic effects LC 50 Lipinski rule

o-Aminoazotoluene 7340 2.46 Class 2(persistent chemical)

-0.31 YES

Imagine 5291 -0.83 Class 2(persistent chemical)

1.84 NO


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and 2, their AutoDock binding free energies ( Gb, in kilocalories per moles) and inhibition

constants were obtained. Free energy signifies the quantity of energy that is available for the

work. Among these 7 compounds, the one exhibited the lowest free energy was o-

Aminoazotoluene -6.02 kcal/mol which is representative of the highest potential binding

affinity with the binding site of EGFR, tyrosine domain. Binding energy signifies Docking

studies of the drugs that are already available in the market and same receptor is shown in

table .3. Best binding affinity was shown by imatinib that is -7.47.Further toxicity testing of

imatinib and o-Aminoazotoluene was done via open tox. Open tox results signify that

geraniol analog is having higher value of x-log p and lower ecotoxic effect in comparison to

the imatinib. It also follows, lipinski rule of five.

Docking Results Of Ligands

Fig 1. 6053 Fig 7340


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Fig 17211 Fig 643820


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Fig 5282109 Fig 535648


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Fig 6430784

Docking Result Of Drugs

Fig.1.5291

Fig.2. 123631


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Fig.3.208908

fig.4.3062316

4) CONCLUSION

Phytochemicals are considered as an ablaze arena for treatment of various diseases. In this

study, we described rational strategy for identification of novel tyrosine kinase inhibitors of

natural origin via using virtual screening along with docking studies. Molecular docking

study was performed to improve the reliability and accuracy of virtual screening. Analysis of

molecular interaction was carried out between different geraniol analog and the target protein

via docking. The one with adequately minimum energy was of o-Aminoazotoluene -6.02.

Further comparison on the scale of ecotoxicity has given an insight that geraniol analog is

less toxic and have better druggability than listed drug ,and could be explored further to a

potent drug.

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