Indian Journal of Geo-Marine Sciences

Vol. 42(5), September 2013, pp. 653-658

Anti cancer activity prediction of secondary metabolites from marine sponge

discodermia calyx: An in silico approach
Sumit Raj1 & D Inbakandan2
1
Department of Bioinformatics, Sathyabama University, Chennai 119, India
2
Center for Ocean Research, Sathyabama University, Chennai 119, India
[E-mail: inbakandan@gmail.com]

Received 12 May 2012; revised 11 August 2012

A molecular docking analysis was carried out followed by Molecular Dynamics (MD) simulation studies on the
secondary metabolites from a marine sponge Discodermia calyx in order to identify their bioactive targets acting towards
cancer. Over expression of Epidermal Growth Factor Receptor (EGFR) results in triple negative breast cancer. Hence, a
docking investigation was carried out in order to predict the anticancer properties of secondary metabolites from a marine
sponge D. calyx targeting the EGFR. The compounds were further subjected to MD simulation analysis. Docking analysis
reveals that the compounds debromohamacanthin B, tetrahydrofurospongin and deoxytopsentin showed good interaction
with the EGFR receptor forming hydrogen bonds with the tyrosine and arginine residue preventing the binding of EGF to
the EGFR receptor by inhibiting dimerization with a score of 130.13, 139.369 and 114.416 respectively.

[Keywords: Discodermia calyx, EGFR, MD simulations, Docking, Triple negative breast cancer]

Introduction tumor cell growth, proliferation, survival, metastasis,

Marine sponges act as a reservoir of natural bioactive
compounds which act against disease such as cancer.
Marine sponges belonging to the genus Discodermia are
a promising source of diverse chemical metabolites.
These organisms have evolved with great genomic
diversity1. D. calyx is a marine sponge isolated off the
coast of Jeju Island, South Korea by Prof. Chung Ja Sim
of Hannam University, Daejon2. Marine sponge D.calyx
is reported to contain the calyculins3, unique polyketides
bearing nitrogen and phosphorus functions. Secondary
metabolites from sponges have a varied biological
activity in various diseases such as HIV, Inflammatory
disorders, Tumor etc. Discodermolide is a recently
discovered polyketide natural product obtained from
D. calyx found to be a potent inhibitor of tumor cell
growth. Molecules carbon skeleton is made up of eight
polypropionate and four acetate units with
13 stereocenters4.
EGFR and related EGBB family of proteins are
known to play an important role in the cancerous
conditions5. Expression of EGFR has been diagnosed
in many human related carcinoma studies along with
its role in carcinoma prognosis. Epidermal growth
factor (EGF) is the prototype of a family of peptide
ligands that bind to cell membrane receptors and
activate intracellular signaling pathways to control
and angiogenesis. EGF receptor (EGFR, ErbB1, or
HER1) is one of a four-member family of
transmembrane receptors that, similar to HER2, is
often over expressed in cancer cells. EGFR
therefore, represents a good target for the
development of novel anticancer therapies6,7. EGFR
are single chain transmembrane polypeptide proteins
possessing three different domains: (a) the extracellular
domain, which binds to ligands that activate the
receptor, (b) the transmembrane domain that is
involved in dimerization interaction between receptors,
and (c) the intracellular tyrosine kinase domain that
phosphorylates tyrosine residues on substrate proteins.
The crystal structures of extracellular domains of
EGFR, HER-2 and HER-3 show that they consist of
four sub domains (I IV)8,9. When ligand binds to the
extracellular domain of the EGFR it undergoes a
conformational change allowing activation either by
homodimerization or heterodimerization with other
members of the erbB family and phosphorylation of
several tyrosine residues10.
Materials and Methods
The protein structure was downloaded from
Protein Data Bank (PDB)11 with PDB id 1IVO12
(Fig. 1). The crystal structure of EGFR (PDB 1IVO)
contains 2:2 EGF: EGFR complex per asymmetric unit.
654 INDIAN J. MAR. SCI., VOL. 42, NO. 5, SEPTEMBER 2013

In the 2:2 EGF: EGFR complex, each EGF molecule is was then subjected to a 5 picoseconds (ps) heating
bound to only one of the two EGFR molecules, two 1:1 step from 0 to 300 K, a 150 ps equilibration step at
EGF: EGFR complexes are dimerized12. 300 K, and finally 150 ps of full MD production at
18 secondary metabolites (Table 1) reported 300 K with NPT ensemble. All simulation steps were
to be isolated from the sponge D. calyx was run with a time step of 1 fs. Full MD trajectory was
collected after literature survey2,13. The structure of considered for analysis. Interaction energy of
the 18 metabolites was drawn in ACD Chemsketch14 inhibitors with each individual residue in the binding
and was saved in .mol format in order to use as input site was estimated on the Simulation package.
for ligand set for docking studies.
Results and Discussions
Docking analysis was done using Accelrys
The protein structure was downloaded from PDB
Discovery Studio and the results in terms of hydrogen
and was docked with the prepared ligand set of
bonding and the scoring functions were noted. In
18 secondary metabolites from D. calyx. Of the
order to investigate further details of the interactions
18 compounds docked with the EGFR receptor there
between the protein and the ligand MD simulation
were 3 compounds namely Debromohamacanthin B,
was performed using the Simulation package in
tetrahydrofurospongin and deoxytopsentin showed
Discovery Studio 2.115 (Accelrys Inc., CA) with
interaction by binding at the EGF binding site
CHARMm force field. Briefly, the complex was
residues with a dock score of 130.13, 139.369 and
solvated in a water spherical boundary with harmonic
114.416 thereby preventing the binding of EGF to the
restraint using an inhibitor as a centre of mass and
EGFR receptor by inhibiting dimerization (Figs 2-4).
subsequently energy-minimized by the steepest
descent and conjugate gradient methods until the
system reached 0.001 kcal/mol convergence. System

Fig. 3Interaction of EGFR with tetrahydrofurospongin with a

docking score of 139.369 forming a total of four H bonds

Fig. 13D structure of EGFR downloaded from PDB having PD

id 1IVO

Fig. 2Interaction of EGFR with Debromohamacanthin B with a Fig. 4Interaction of EGFR with deoxytopsentin with a docking
docking score of 130.13 forming a total of five H bonds score of 114.416 forming a total of four H bonds
 RAJ & INBAKANDAN: ANTI CANCER ACTIVITY PREDICTION OF SECONDARY METABOLITES 655

Table 1List of the metabolites from D. calyx under study (Courtesy: Dr. Jee H. Jung)
S no. Name of the metabolite Structure

1 Ent-kurospongin

2 Tetradehydrofurospongin-1

3 Deoxytopsentin

4 Isobromodeoxytopsentin

5 Bromodeoxytopsentin

6 cis-3,4-Dihydrohamacanthin B

7 Hamacanthin B

8 6-Debromohamacanthin B

contd
656 INDIAN J. MAR. SCI., VOL. 42, NO. 5, SEPTEMBER 2013

Table 1List of the metabolites from D. calyx under study (Courtesy: Dr. Jee H. Jung) contd
S no. Name of the metabolite Structure

9 HamacanthinA

10 6-DebromohamacanthinA

11 Icadamide C

12 Icadamide A

13 Theopedrin K

14 Theopedrin L

15 Mycalamides A

16 Mycalamides B

contd
 RAJ & INBAKANDAN: ANTI CANCER ACTIVITY PREDICTION OF SECONDARY METABOLITES
Table 1List of the metabolites from D. calyx under study (Courtesy: Dr. Jee H. Jung) contd
S no. Name of the metabolite
17 Icadamide S
18 Icadamide A
Fig. 5Time Vs Energy graph obtained after simulation studies
confirms the convergent behavior of the systems during the entire
course of simulation. (The time is in ps and energy in kcal/mol)
Hydrogen bonds were found to form between the
Tyrosine of one monomer with the Arginine residue
which is important for structural stability.
In MD Simulation studies Solvation protocol
allows us to create an explicitly solvated system using
CHARMm force field. Water molecules and
optionally counter ions can be added to a molecule.
The solvated model had 27685 solvent molecules
generated by this protocol in Discovery Studio 2.1.
Root mean square deviation (RMSD) of backbone
atoms of the protein revealed that the protein was very
stable with an average RMSD value of 0.14 nm
throughout the simulation time whereas the inhibitor
complexes were stable during the second half of the
simulation time (2500-5000 ps). Computed energy
value was found to be -63113.4350 kcal/mol. Total
energy with respect to time was found to decrease on
a constant basis (Fig. 5). These changes in RMSD
657
Structure
states that the binding of the ligand seems to increase
the conformational flexibility of the receptor confirms
the convergent behavior of the systems during the
entire course of simulation and results are reliable
for further studies.
Conclusion
Some of the compounds from the sponge D. calyx
showed high binding affinity towards the EGFR
receptor. Docked structure fits into the active site
region of the receptor accurately. This shows that the
bioactive molecules identified from this species can
be further used as leads for designing anti-cancer
drugs. Substructure-pharmacophore studies of these
top scored ligands might help in building more
specific and high affinity lead molecules. Such results
may help to corroborate the present findings.
However, wet lab experiments involving chemical
synthesis and testing the designed molecules in vivo
using specific cell lines would be necessary to arrive
at definite conclusions.
Acknowledgement
Authours thank the Chancellor and Directors,
Sathyabama University, Chennai for their support to
carry out the research and Department of
Bioinformatics, Sathyabama University, Chennai for
providing support in terms of computing facilities.
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