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Interdiscip Sci Comput Life Sci

DOI 10.1007/s12539-017-0252-5

ORIGINAL RESEARCH ARTICLE

Identification of Lead Molecules in Garcinia mangostana L.


Against Pancreatic Cholesterol Esterase Activity: An In Silico
Approach
George Kadakasseril Varghese1 • Rini Abraham2 • Nisha N. Chandran3 •

Solomon Habtemariam4

Received: 6 October 2016 / Revised: 8 July 2017 / Accepted: 12 July 2017


Ó Springer-Verlag GmbH Germany 2017

Abstract Hypercholesterolemia is one of the major risk the prospects of the identified lead molecules as potential
factors for the development and progression of drug candidates.
atherosclerosis. Hence, inhibitors of cholesterol absorption
have been investigated for decades as a strategy to prevent Keywords Garcinia mangostana  Cholesterol esterase 
and treat cardiovascular diseases associated with hyperc- AutoDock  GOLD  Epicatechin  Euxanthone 
holesterolemia. Cholesterol esterase (CEase) in pancreatic Tetrahydroxy-xanthone
juice plays a vital role in the hydrolysis of dietary
cholesterol esters to cholesterol and fatty acids. Since
inhibition of CEase might lead to a reduction of cholesterol 1 Introduction
absorption, an attempt is made in this study to identify lead
molecules of Garcinia mangostana by the in silico Hypercholesterolemia is one of the risk factors for the
approach. The study employed software applications viz., development and progression of atherosclerosis that lead to
AutoDock 4.2 and GOLD Suite of Programs 5.2. The study cardiovascular diseases [1, 2]. Hence, management of
revealed the efficacy of three compounds viz., epicatechin, hypercholesterolemia is suggested as a strategy to prevent
euxanthone, and 1,3,5,6-tetrahydroxy-xanthone, which cardiovascular disease. Many drugs such as statins have
exhibited least binding energy in AutoDock and moderate been developed for this purpose, which block the enzyme
scoring in GOLD. The molecular properties as well as HMG-CoA (5-hydroxy-3-methylglutaryl-coenzyme A)
biological activity of these three compounds were pre- reductase, that is essential for the biosynthesis of choles-
dicted by molinspiration prediction tool. The results show terol [3]. However, statin drugs induce adverse side effects
the crucial role of polyphenolic compounds to limit the [4] including allergic reactions like skin rashes, heartburn,
activity of CEase. The drug-likeness prediction revealed dizziness, abdominal pain, constipation [5], decreased
sexual desire, hepatic dysfunction, renal insufficiency,
& George Kadakasseril Varghese
hypothyroidism, and premature aging [6].
kvgeorge58@yahoo.in Dietary cholesterol contains free and esterified choles-
terol. Intake of high amounts of saturated fats is believed to
1
Department of Botany, St. Berchmans’ College, be directly related to hypercholesterolemia and suscepti-
Changanassery, Kerala, India
bility to atherosclerosis [7]. Consequently, dietary and
2
School of Environmental Sciences, Mahatma Gandhi biliary cholesterol absorption inhibitors such as ezetimibe
University, Kottayam, Kerala, India
have been introduced as a new class of lipid-lowering
3
Biotechnology and Bioinformatics Division, Saraswathy drugs [8]. Lipids are a broad group of diverse naturally
Thangavelu Centre, Jawaharlal Nehru Tropical Botanic
occurring organic compounds that play major roles in the
Garden & Research Institute, Thiruvananthapuram, Kerala,
India body by serving as energy sources, components of cellular
4 structures like cell membranes, and acting as signaling
Pharmacognosy Research Laboratories, Medway School of
Science, University of Greenwich, KENT, molecules such as hormones (e.g. steroids). Structurally,
Medway ME4 4TB, UK dietary lipids are composed of glycerol esterified by fatty

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acids and/or sterols to give either fat or oil depending on of cardiovascular drugs viz., lovastatin, simvastatin,
the length of the fatty acid components. Lipids composed nifedipine, amoldipine besylate, hydralazine hydrochloride
of long chain fatty acids generally appear as solid fat, while [20] Cordyceps sinensis [21], and Camellia sinensis [22]
those with shorter fatty acids are liquids and hence called against CEase were reported in the literature. Krause et al.
oils. When the fatty acid components of fats/oils are made [23] also showed the beneficial effect of the phenoxy
of one (mono) or many (poly) double bonds, they are called phenyl carbamate synthetic novel inhibitor of CEase,
unsaturated fatty acids which are generally considered a WAY-121,898, in normal and cholesterol-fed rats and
healthier option when compared to the saturated fatty dogs. John et al. [13] identified potential pancreatic CEase
acids. Lipid digestion in the gut involves a series of inhibitors by pharmacophore modeling, virtual screening,
enzymatic processes directed in releasing fatty acids and and optimization techniques and developed a pharma-
sterol from their esterified (glycerol esters) forms. In this cophore model based on chemical features of certain
connection, one of the key enzymes involved in lipid known CEase inhibitors.
metabolism is the carboxyl ester lipase or cholesterol In traditional systems of medicine, a large number of
esterase (CEase) or cholesterol ester lipase (also known as medicinal plants have been used for the treatment of
pancreatic lysophospholipase or bile salt-stimulated cardiovascular diseases. The antihyperlipidemic activity
lipase). It belongs to the a/b hydrolase family of glyco- of medicinal plants like Aegle marmelos, Musa para-
protein enzymes [9–11] and is responsible for the hydrol- disiaca, Solanum trilobatum, Alpinia officinarum, Cyn-
ysis of dietary cholesterol esters, fat soluble vitamins, odon dactylon [24], Allium sativum [25], Achyranthes
triglycerides, and phospholipids. The CEase is synthesized aspera [26] Cassia fistula [27], and Commiphora mukul
in the acinar cells of the pancreas and it constitutes 1–2% [28] were reported in the literature. Screening of choles-
of total protein in pancreatic juice. The enzyme is stored in terol esterase activity of the bioactive compounds of
zymogen granules from where it is released into the Terminalia cuneata was also reported in a recent inves-
intestinal tract and activated by primary bile salts [12]. In tigation [29]. Besides, Asmaa and Ream [30] evaluated
addition to the pancreas, CEase has been found in other the in vitro screening of the pancreatic cholesterol ester-
tissues such as small intestine, liver, brain, and placenta of ase inhibitory activity of selected medicinal plants
numerous species including humans. Its presence is also (Ecballium elaterium, Pinus brutia, Plantago lanceolata,
noted in the breast milk, which ensures efficient triglycerol Schinus molle, and Hedera helix) grown in Syria. Inhi-
utilization of the newborn babies [12, 13]. Milk CEase is bition of pancreatic CEase activity by natural compounds
postulated to substitute for the pancreatic enzyme in the is, therefore, reckoned as a new target for the treatment of
neonatal gastrointestinal tract before maturation of the hyperlipidemia.
pancreas [14]. Garcinia mangostana L (family, Clusiaceae) is rou-
The CEase has structural similarity with serine proteases tinely employed in traditional medicine to treat inflam-
and its X-ray crystal structure shows similarity with lipases mation, diarrhea [31], skin infections, wounds, arthritis
[15]. Its active site includes a catalytic triad (SER-194, and hemorrhoids [32, 33] among others. Pharmacological
HIS-435, ASP-320) that serves as a nucleophilic and gen- studies revealing the antioxidant [34], anti-tumoral/anti-
eral acid–base catalytic entity [9, 16, 17]. Furthermore, its inflammatory [35, 36] antidiabetic [37, 38], cardiopro-
active site possesses an oxyanion hole (Gly-107, Ala-108, tective [39], and antimicrobial/antiviral/antimalarial
Ala-195) residues [13]. Studies conducted by Howles et al. [32, 40, 41] activities have been reported for G. man-
[12] in CEase gene-targeted transgenic mice revealed a gostana. Some studies conducted by Williams et al. [42],
reduced uptake of cholesterol ester suggesting the crucial Hanna et al. [43], Obolsky et al. [44], and Adiputro et al.
role of this enzyme in intestinal fat digestion/absorption. It [39] further suggested the prospect of developing G.
has also been suggested that it may provide the transport mangostana as a potential drug candidate for the man-
function and delivery of cholesterol from micelles to agement of lipid profile. In this regard, the most relevant
enterocytes [18]. The participation of CEase along with plant parts, the fruits, have been shown as rich sources of
phospholipase A2 in the hydrolysis of lecithin to lysole- bioactive compounds [45–47] and some of these com-
cithin, which is required for the formation of intestinal pounds have already been shown to improve the lipid
micelles and delivery of free cholesterol, has also been profile in blood [48–50]. As these compounds have not
demonstrated [19]. Hence, inhibition of this enzyme might previously been subjected to in silico docking evaluation
lead to a reduction of cholesterol digestion/absorption for CEase activity, the present study aims to identify lead
which in turn reduces the concentration of serum molecules through such modeling study. The binding
cholesterol. affinity of the phenolics (flavonoids, anthocyanins, and
In the above context, a few studies were reported on xanthones) and benzophenones of G. mangostana against
inhibition of CEase. In vitro studies on inhibitory activity CEase is systematically presented.

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2 Objective 3.4 AutoDock

To identify potential lead molecules of G. mangostana with This tool makes use of Monte Carlo simulated annealing as
inhibitory effect on CEase through molecular docking well as Lamarckian Genetic algorithm for the generation of
using Auto Dock and GOLD. possible orientations of ligand. Docking was carried out
following the AutoDock procedure [51]. The 3D crystal
structure of cholesterol esterase (PDB entry: 1F6W) is a
3 Materials and Methods tetramer. The C and D chain of the target molecule was
kept whereas the chains A and B were unmerged and
3.1 Preparation of Macromolecule deleted because the tetramer was symmetrical as reported
in the literature [52].
The 3D crystal structure of the protein, cholesterol esterase
(Fig. 1) (PDB ID: 1F6W) a tetramer was retrieved from the 3.5 GOLD
RCSB Protein Databank and saved in the PDB file format.
Its active residue, Ser-194 was identified through Pocket- Genetic algorithm was implemented in GOLD 5.2 that was
Finder and Q-Site Finder. applied to calculate the possible conformations of the
ligand that binds to the protein. The procedure adopted by
3.2 Preparation of Ligands earlier researchers [53] was followed for analysis. The
genetic algorithm parameters used in this study are: pop-
The structural features of 28 phytochemicals selected for ulation size—100; number of islands—5; niche size—2;
the study were collected from the published works [44] of selection pressure—1.1; migrate—2; number of opera-
G. mangostana (Table 1; Fig. 2). The canonical SMILES tors—100,000; mutate—95; cross over—95. During
of these molecules were obtained from PubChem (www. docking process, a maximum of ten different conforma-
ncbi.nlm.nih.gov/pubchem) and 3D structures were gener- tions was considered for the ligand. The pose with highest
ated using CORINA, the online 3D generation software. binding score was used for further analysis.
The 3D structure of eight molecules were not available in
any database, hence the structures of those molecules were 3.6 Drug-Likeness Prediction
drawn and generated 3D using ChemSketch and CORINA,
respectively. 3.6.1 Molinspiration Property Prediction Tool

3.3 Docking To analyze the drug-likeness of the hit molecules viz., epi-
catechin, euxanthone, and 1,3,5,6-tetrahydroxy-xanthone of
Docking was done using an open access software appli- G. mangostana fruit rind extract, these molecules were
cation package AutoDock 4.2 and a commercial docking submitted to the open access molinspiration property pre-
software application Gold 5.2. diction tool (www.molinspiration.com). This tool analyzes
the molecular properties based on Lipinski’s rule of five and
provides the violation in the particular property. The soft-
ware was used to analyze the molecular properties such as
miLogP, total polar surface area (TPSA), drug-likeness,
MW, ON, OHNH, ROTB, and the volume from the three-
dimensional structure of the given molecule. MiLogP (Oc-
tanol/water partition coefficient) is the parameter used to
predict the permeability of the molecule across the cell
membrane and it is calculated through the methodology
developed by molinspiration, as a sum of fragment-based
contributions and correction factors. The miLogP was
obtained by fitting calculated logP with experimental logP
for a training set of drug-like molecules which describes the
oral activity of a molecule. The TPSA is used to predict drug
absorption that includes intestinal absorption, bioavailabil-
ity, Caco-2 permeability, and blood-barrier penetration. It is
calculated through the sum of fragment-based contributions
Fig. 1 3D structure of pancreatic cholesterol esterase of O- and N-centered polar fragments and the surface areas

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Table 1 Phytochemicals of G. mangostana selected for the docking study


SI no. Major classes Name of phytochemicals Mol. formula and mol.
weight (g/mol)

I Phenolic compounds Epicatechin C15H14O6 (290.2680)


(a) Flavanoid: Flavane
(b) Flavonoid: Cyanidin-3-glucoside C21H21O11 (449.3848)
Anthocyanin Chrysanthemin C21H21O11 (449.3848)
(c) Xanthones Alpha-mangostin C24H26O6 (410.4596)
Beta-mangostin C25H28O6 (424.4862)
BR-Xanthone C23H24O6 (396.4313)
Calaba xanthene C24H24O5 (392.4438)
Cudraxanthone C19H18O5 (326.3429)
Euxanthone C13H8O4 (228.2041)
Gamma mangostin C23H24O6 (396.4342)
Garcinone D C24H28O7 (428.4709)
Gartanin C23H24O6 (396.4365)
Isomangostin C24H26O6 (410.4582)
Mangostanol C24H26O7 (426.459)
Mangostenol C24H26O7 (426.459)
Mangostanin C24H26O7 (426.459)
Smeathxanthone A C23H24O6 (396.4332)
Trapezifolixanthon C23H22O5 (378.4177)
Tovophylline A C28H30O6 (462.534)
Tovophylline B C28H28O6 (460.5183)
1,3,5,6-Tetrahydroxy-xanthone C13H8O6 (260.199)
1,5-Dihydroxy-2-isoprenyl-3-methoxyxanthone C19H18O5 (326.343)
6-O-methylmangostanin C25H26O6 (422.4703)
8-Deoxy gartanin C23H24O5 (380.4)
8-Hydroxycudraxanthone G C24H26O6 (410.172)
II Benzophenones Kolanone C33H42O4 (502.6841)
Malcurin C13H10O6 (262.2149)
Garcimangosone D C19H20O9 (392.3521)

occupied by hydrogen bound oxygen and nitrogen atoms. xanthones) and benzophenones were docked against CEase
The number of rotatable bonds (NORTB) is a topological enzyme at its active site, Ser-194 employing AutoDock, and
parameter which defines the measures of molecular flexi- GOLD programs, which provided the conformational space of
bility as well as oral bioavailability of the drug molecule the ligands using genetic search algorithm in combination
[54]. Molecular volume determines transport of molecules with various scoring functions. The AutoDock results gener-
such as blood-barrier penetration and intestinal absorption ated for ligands in terms of docking energy score,
[55]. The bioactivity score of epicatechin, euxanthone, and B-5 kcal/mol were accepted since their lower AutoDock
1,3,5,6-tetrahydroxy-xanthone was then calculated for scores generally indicate better interactions with the targeted
GPCR ligand, ion channel modulator, kinase inhibitor, and enzyme. On the other hand, the GOLD docking results gen-
nuclear receptor ligand using the molinspiration software erated in terms of higher values of fitness are considered
applications. because it shows better interactions of the complexes. All the
catalytic residues were present in active site pocket of the
enzyme, so as to be functional for the formation of stable in-
4 Results teractive bonds with ligand molecules. The neighboring
residues of active pocket residue (Ser-194) are: GLU193,
In the present investigation, 28 phytochemical compounds of ALA195, GLU197, ALA198, GLN219, SER220, GLY221,
G. mangostana belonging to two major classes of secondary TYR125, and HIS435. The results generated in terms of both
metabolites viz., phenolic compounds (flavanoids and AutoDock and GOLD scores (Table 2) indicate better

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Fig. 2 Structures of phytochemicals in G. mangostana selected for the docking study

possibility of three molecules viz., epicatechin, euxanthone, 1,3,5,6-tetrahydroxy-xanthone (-5 kcal/mol), and euxan-
and 1,3,5,6-tetrahydroxy-xanthone to be developed as thone (-5.68 kcal/mol) showed good binding energy. Further
potential drug molecules. The study revealed higher activity analysis of the docked structures revealed the formation of
for the flavanoid, flavane, and xanthone compounds three strong hydrogen bonds (GLU193:H34, TYR125:H28
(B-5 kcal/mol) and least activity for the flavanoid, antho- and HIS435:HE2) between the compound epicatechin and
cyanin, and benzophenones. Of the 28 phytochemical com- CEase (Fig. 3). With respect to xanthone compounds viz.,
pounds of G. mangostana, epicatechin (-5.63 kcal/mol), 1,3,5,6-tetrahydroxy-xanthone and euxanthone, hydrogen

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Table 2 Docking results by using AutoDock and GOLD


Lead molecule AutoDock GOLD score
Binding energy (kcal/mol) Hydrogen bond Bond length (Å) Bond type KI (lM)

Epicatechin -5.63 GLU193:H34 2.196 O–H..O 74.09 46


TYR125:H28 1.702 O–H..O
HIS435:HE2 1.947 O..H–N
Euxanthone -5.68 HIS435:HE2 1.947 O..H–N 155.55 43
1,3,5,6-tetrahydroxy-xanthone -5 HIS435:HE2 1.947 O..H–N 418.53 42

peo/). In our result, the selected candidate ligands show


MiLog value \5.0 and thus can be concluded to have good
permeability. In respect of TPSA, the selected three com-
pounds were within the limit 140 Å, which implies that
molecules are fulfilling the optimal requirement for drug
absorption. After the prediction of molecular properties,
the tool compared it with Lipinski’s rule of five and found
that the three selected lead molecules did not show any
violations. Hence the drug-likeness prediction ensured the
potential of the selected lead molecules as drug candidates.
Generally, the bioactivity score is directly proportional
to the activity of a molecule as a drug. The molecule with
bioactivity score higher than 0.00 can be considered as a
higher possibility for biological activity. The score between
-0.50 and 0.00 shows moderate and the value less than
-0.50 may be inactive. The bioactivity score of the
selected lead molecules (Table 4) show very good bio-
logical activity for the compound epicatechin and moderate
Fig. 3 Molecular interaction of epicatechin with cholesterol esterase
(hydrogen bonds can be seen in dotted lines) biological activity for euxanthone and 1,3,5,6-tetrahy-
droxy-xanthone. All the lead molecules show potential
bonds were observed between HIS435 & HE2 and HIS435 & biological activity as enzyme inhibitors and nuclear
HE2 at respective sites as shown in Figs. 4 and 5. On the basis receptor ligands. When the compound epicatechin shows
of the present study, epicatechin, 1,3,5,6-tetrahydroxy-xan- higher possibility for biological activity with respect to all
thone, and euxanthone compounds of G. mangostana were bioactivity parameters, euxanthone and 1,3,5,6-tetrahy-
recommended as potential leads for further investigations that droxy-xanthone show moderate bioactivity with respect to
may lead to the discovery of a new drug for GPCR ligand, ion channel modulator, and kinase inhibitor.
hypercholesterolemia. However, it is to be noted that the compound euxanthone
Molinspiration prediction of drug-likeness and bioac- violates protease inhibitor activity (-0.52). In short, the
tivity score with special reference to the selected three result generated in this study is in agreement with the
ligand molecules of G. mangostana are shown in Tables 3 expected outcome. On the basis of the present study, epi-
and 4. Drug-likeness properties viz., MiLogP, TPSA, catechin, 1,3,5,6-tetrahydroxy-xanthone and euxanthone
number of atoms, molecular weight, number of hydrogen compounds of G. mangostana were recommended as
bond acceptors (expressed as the sum of N and O atoms), potential leads for further investigations that may lead to
number of hydrogen bond donors (total number of nitro- the discovery of new drug for hypercholesterolemia.
gen–hydrogen and oxygen–hydrogen bonds, expressed as
the sum of OH and NH groups), number of violations,
number of rotatable bonds, and molecular volume of the 5 Discussion
lead molecules were generated with the help of software,
molinspiration drug-likeness score online (www.molin It has been firmly established that hypercholesterolemia has
spiration.com). For compounds to have a rational proba- positive relationship with atherosclerosis and ischemic heart
bility of being well absorbed, their logP value must not be disease [56]. Therefore, the inhibition of enzymes that con-
greater than 5.0 (http://www.organic-chemistry.org/prog/ trols cholesterol absorption and transportation is considered a

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Fig. 4 Molecular interaction of


1, 3, 5, 6-tetrahydroxy-xanthone
with cholesterol esterase
(hydrogen bond can be seen in
dotted lines)

Fig. 5 Electrostatic interaction


of euxanthone with residues at
active site

Table 3 Prediction of drug-likeness properties of lead molecules by molinspiration


Lead molecules MiLogP TPSA Atoms MW #ON #OHNH #Violations #ROTB Volume

Epicatechin 1.37 110.37 21 290.27 6 5 0 1 244.14


Euxanthone 2.80 70.67 17 228.20 4 2 0 0 188.61
1,3,5,6-tetrahydroxy-xanthone 2.01 11.12 19 260.20 6 4 0 0 204.65

Table 4 Bioactivity score of the selected lead molecules


Lead molecules GPCR Ion channel Kinase Nuclear receptor Protease Enzyme
ligand modulator inhibitor ligand inhibitor inhibitor

Epicatechin 0.41 0.14 0.09 0.60 0.26 0.47


Euxanthone -0.31 -0.14 -0.14 0.06 -0.52 0.20
1,3,5,6-Tetrahydroxy-xanthone -0.29 -0.22 -0.02 0.21 -0.49 0.31

good target for reducing blood cholesterol. Evidence from the polyphenols in combating the various components of diabetes
in vitro study revealed that polyphenols such as gallic acid, (e.g. inflammation, lipid metabolism, oxidative status, etc.)
catechin, and epicatechin significantly inhibit CEase in a also makes them good drug candidates in combating cardio-
concentration-dependent manner [48, 57]. These polyphenols vascular and or hyperlipidemia diseases [50, 59]. The sug-
have been shown to inhibit the intestinal digestion and gestion that epicatechin can act as a potent insulin receptor
absorption of dietary lipids [49], possibly through inhibition of activator was corroborated by docking studies [60]. Recent
CEase activity. Inhibitory activity of selected flavonoid studies also suggest inhibitory activity of tea flavonoid that is
compounds like apigenin, epipervilline, curcumin, etc. has mediated through its irreversible binding with the active fatty
also been reported [58].The multifunctional role of acid pocket, Ser-194, of CEase [22].

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It is also assumed that the basic benzopyran ring struc- the lead molecules ensured the potentiality of the lead
ture of the flavonoid nucleus is responsible for the CEase molecules as a drug. However, theoretical prediction of
inhibitory activity. The three compounds identified as lead drug-likeness only gives higher probability of its activity in
molecules viz., epicatechin, euxanthone, and 1,3,5,6 a biological system. Hence, further in vitro/in vivo and
tetrahydroxy-xanthone are less bulky with less steric hin- clinical studies are needed to propose these molecules as
drance and hence can easily get accommodated in the efficient drugs.
active site of the enzyme. Besides, the hydrogen bonding
interaction enhances aromaticity of these compounds. As Acknowledgements The corresponding author acknowledges
KSCSTE for Emeritus fellowship and financial assistance. We also
previously reported [61–63], hydrogen bonding interaction acknowledge Rev. Dr. Tomy Joseph Padinjareveettil (Principal, SB
increases cyclic 4n ? 2 p electron delocalization which College, Changanassery), Dr. P.G. Latha, and Dr. P. N. Krishnan
simultaneously enhances aromaticity. On the other hand, (Jawaharlal Nehru Tropical Botanic Garden & Research Institute,
bulkiness of the other molecules selected for the study Thiruvananthapuram) for their comprehensive help and support.
enhances steric strain that further increases energy of the
system that does not favor the reaction.
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