Hindawi Publishing Corporation

BioMed Research International

Volume 2016, Article ID 3187647, 14 pages
http://dx.doi.org/10.1155/2016/3187647

Research Article
Treating Diabetes Mellitus: Pharmacophore Based Designing of
Potential Drugs from Gymnema sylvestre against Insulin
Receptor Protein

Mohammad Uzzal Hossain,1 Md. Arif Khan,1 S. M. Rakib-Uz-Zaman,2

Mohammad Tuhin Ali,3 Md. Saidul Islam,4 Chaman Ara Keya,5 and Md. Salimullah4,6
1
Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University,
Santosh, Tangail 1902, Bangladesh
2
Department of Genetic Engineering and Biotechnology, Life Science Faculty, Shahjalal University of Science and Technology,
Kumargaon, Sylhet 3114, Bangladesh
3
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
4
National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
5
Department of Biology and Chemistry, North South University, Bashundhara, Dhaka 1229, Bangladesh
6
Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh

Correspondence should be addressed to Md. Salimullah; [email protected]

Received 25 November 2015; Accepted 11 January 2016

Academic Editor: Maxim P. Evstigneev

Copyright © 2016 Mohammad Uzzal Hossain et al. This is an open access article distributed under the Creative Commons
Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is
properly cited.

Diabetes mellitus (DM) is one of the most prevalent metabolic disorders which can affect the quality of life severely. Injectable
insulin is currently being used to treat DM which is mainly associated with patient inconvenience. Small molecules that can act
as insulin receptor (IR) agonist would be better alternatives to insulin injection. Herein, ten bioactive small compounds derived
from Gymnema sylvestre (G. sylvestre) were chosen to determine their IR binding affinity and ADMET properties using a combined
approach of molecular docking study and computational pharmacokinetic elucidation. Designing structural analogues were also
performed for the compounds associated with toxicity and less IR affinity. Among the ten parent compounds, six were found to have
significant pharmacokinetic properties with considerable binding affinity towards IR while four compounds were associated with
toxicity and less IR affinity. Among the forty structural analogues, four compounds demonstrated considerably increased binding
affinity towards IR and less toxicity compared with parent compounds. Finally, molecular interaction analysis revealed that six
parent compounds and four analogues interact with the active site amino acids of IR. So this study would be a way to identify new
therapeutics and alternatives to insulin for diabetic patients.

1. Background around the globe with an expected projection of 366 million

cases in 2030 compared to 171 million in 2000 [4]. Among
Diabetes mellitus (DM) is a group of metabolic diseases in the cases, the city dwellers of developing countries are likely
which there are high blood sugar levels or hyperglycemia over to be the most affected group [4]. Diabetes is a common
a prolonged period. Type 2 diabetes mellitus (T2DM) is the scenario in the South and East Asia Region predominantly in
most prevalent (95%) one compared to type 1 (T1DM) [1]. In Bangladesh, India, Sri Lanka, Bhutan, Mauritius, and Mald-
case of type 1 body fails to produce insulin, whereas in type ives. In 2013, Saquib et al. reported that there are nearly 72
2 body shows resistance to insulin. Also, alteration of many million adult diabetics in these countries which will be raised
genes and their products may contribute in T2DM [2, 3]. to 123 million by 2035 [5]. The very same cross-sectional study
DM is one of the prime concerns of morbidity and mortality conducted among 402 middle class Bangladeshi citizens also
2 BioMed Research International

reveals that as much as 35% of them have T2DM and 45% GS4, plays a very significant role in the regulation of both type
have metabolic complications [5]. 1 and type 2 diabetes [24, 25].
Chronic hyperglycemia in DM leads to the damage Very few studies have been conducted on plant derived
of kidneys, nervous system, eyes, heart, and blood vessels compounds with pharmacoinformatics elucidation for the
[6]. Acute myocardial infarction and fatal reinfarction are identification of novel therapeutics against diabetes [26, 27].
common with diabetic patients in the acute phase and during In this study, we have considered antidiabetic compounds
the first year of follow-up [7–11]. However, to compensate from G. sylvestre and their analogues as possible drug candi-
the lower level of insulin in blood, administration of insulin dates for insulin receptor. Various computational tools have
injection followed by intensive treatment with multidose been used to perform pharmacoinformatics validations of
subcutaneous insulin can reduce up to 30% of mortality in these compounds as well as to investigate their structural
diabetic patients with acute myocardial infarction [12–14]. (similar and different) analogues [28–36]. Also, Computer
Insulin, secreted from the pancreatic 𝛽-cells, is the most Aided Drug Design (CADD) tools have been used for the
studied peptide hormone for its importance to control glu- structural property as well as identification of interaction
cose homeostasis. This 51-aa hormone binds to its transmem- between insulin receptor and candidate drugs [28, 32–35, 37–
brane 𝛼2 𝛽2 glycoprotein insulin receptor (IR). Intracellular 40]. Finally, AutoDock tools were utilized for the assessment
tyrosine kinase domain of IR is activated by insulin binding of ligand-protein interaction [38, 39]. This inclusive in silico
and triggers cascade of intracellular signaling pathways which analysis may provide insights into the understanding of drug-
eventually enhance cellular uptake of glucose from circu- protein interaction and to design effective antidiabetic drugs.
lation [15, 16]. Diabetes mellitus (DM) is the complication
caused either by the poor tissue responsiveness to insulin or
by the metabolic malfunction of insulin production. Type 1
2. Materials and Methods
DM is an autoimmune disorder where pancreatic 𝛽-cell is The outline of this study was shown in Figure 1.
destroyed by the immune system which causes insufficient
insulin secretion, whereas type 2 DM is caused by resistance
2.1. Preparation of Target Protein and Selection of Novel Drugs.
of body tissue towards insulin [17, 18]. In both cases, insulin
The 3D (three-dimensional) crystal structure of insulin
injection is necessary to maintain glucose homeostasis.
receptor protein 3LOH used in this study was retrieved from
Although recombinant insulin is now available and the
RCSB (Research Collaboratory for Structural Bioinformatics)
technology for insulin delivery has improved in the recent
past but the discomfort and inconveniency associated with Protein Data Bank (PDB) [28]. The ligands from PDB files
insulin injection cannot be denied. Additionally, long term of 3LOH were removed using Discovery Studio 4.0 client
insulin injection leads to the development of cutaneous (http://accelrys.com/products/discovery-studio/). The poly-
complications such as allergy, lipoatrophic area development, peptide chains (A, B, C, and D) of 3LOH were removed, and
and injection abscesses [19]. Therefore, the discovery of only E chain (insulin binding domain, ectodomain) of Homo
small molecules that are capable of mimicking insulin action sapiens was saved as PDB file format for further analysis
and can be administered orally would be better alternative (see Supplementary Figure S1 in Supplementary Material
therapies for the diabetic disorder. As of now very little work available online at http://dx.doi.org/10.1155/2016/3187647).
has been done to develop such kind of small molecules. More- After removal of the ligands and chains (A, B, C, and D), chain
over, the identified small molecules have several problems E of insulin receptor 3LOH was effectively used to screen and
such as poor IR specificity or bioavailability. For instance, find out novel molecules for the treatment of diabetes. For
arylalkylamine vanadium salts are strong IR activators but the selection of drugs, existing literatures and databases were
associated with questionable bioavailability, and demethy- searched for plants having antidiabetic properties supported
lasterriquinone B1 (DAQ B1) has insulin mimicking potential by laboratory study for itself and/or its compounds [23–25,
but associated with significant cytotoxicity [20, 21]. 41, 42]. Among many, Gymnema sylvestre, a plant common
Herein, we selected G. sylvestre derived small compounds in South Asia, were selected for the current study. A total
to check their significance to be assigned as potential candi- of ten compounds (Figure 2) were selected from Gymnema
date for IR activators designing. G. sylvestre is a commonly sylvestre based on the following criteria: (i) tested com-
seen herb in South Asian region (India, Sri Lanka, and pounds having antidiabetic (T2DM) effect (Gymnemoside
Bangladesh as well) which is considered as promising source B and Conduritol A) and their analogues (Gymnemoside
of antidiabetic compounds. G. sylvestre derived compounds A and Conduritol B tetraacetate, Conduritol C cis-epoxide
demonstrated considerable antidiabetic results in several analogue, Conduritol D, and Conduritol E tetranitro), (ii)
experiments [22]. Experimental trials have been conducted tested compounds with no antidiabetic effect (Gymnemic
in animal models with G. sylvestre active constituents of acid I, Gymnemic acid II), and (iii) one unique compound,
which insulin-like activity and mechanism of action of hypo- GS4, having antidiabetic effects against both types (T1DM
glycemic principles have been investigated in detail [23]. and T2DM) [24, 25]. The two-dimensional (2D) structure
Amid many, Gymnemic acids III, IV, V, and VII and Gym- of the selected active compounds of this plant was retrieved
nemoside B were recognized as antihyperglycemic active from Click2drug (http://www.click2drug.org/), zinc database
constituents while Conduritol A was found to have cataract- (http://zinc.docking.org/) and PubChem compound [29] as
suppressing effect [24]. Moreover, it has been reported that SDF (Structure Data File) format. Afterwards, the SDF format
another active ingredient from G. sylvestre leaves extract, of the compounds was converted to PDB file by using the
BioMed Research International 3

Selection of plant compounds

through literature searching

Toxic profile
assessment

Toxic
Nontoxic compounds
compounds

Structural ADMET and QSAR

analogues studies

Docking simulation
analysis

Binding and active

site revealing

Val 377,
Glu 438

Figure 1: Schematic representation of the study.

Open Babel [30]. The 3D structure optimization of these (absorption, distribution, metabolism, excretion, and toxicity
compounds was done by the ACD/Chemsketch [31]. structure-activity relationship database) [35] and ACD/I-Lab
[36] handle existing ADMET-associated information from
2.2. Pharmacoinformatics Elucidation. Different computa- the available literature. Default parameters of these online
tional tools and web databases were exploited for the phar- servers are used for the pharmacoinformatics analysis.
macoinformatics elucidation of active compounds that might
have the potentiality to exhibit insulin-like activity by inter- 2.3. Design New Drugs. To improve the antidiabetic activity
acting with the insulin receptor protein. The pharma- of the four tested drugs, novel compounds were designed by
cophoric library screening, ADMET (absorption, distribu- generating their analogues (Supplementary Figure S2). ACD/
tion, metabolism, excretion, and toxicity) and QSAR (quan- Chemsketch [31], Discovery Studio 4.0 clients, and Open
titative structural-activity relationship) properties were car- Babel [30] were employed to accomplish the task.
ried out by Osiris property explorer [32], Molinspiration
[33], AcTor [34], admetSAR [35], and ACD/I-Lab [36]. 2.4. Energy Minimization of Designed Molecules. In designed
Briefly, Osiris property explorer [32] computes various drug structures, an accurate alignment of the side chains is an
related properties like tumorigenicity, mutagenicity, irrita- indispensable requirement in order to link the structural gap
tion, reproductive effect, drug likeness, and drug-score pre- and encompass loop rearrangements, secondary structure
diction based on chemical structure. Molinspiration offers elements, repacking of core residues, and so forth. Here, We
broad range of cheminformatics software tools that support have calculated the free relative binding energies for these
molecule manipulation and fragmentation, calculation of complexes using the YASARA (Yet Another Scientific Artifi-
various molecular properties such as QSAR, molecular mod- cial Reality Application) force field [38]. YASARA uses a full
eling, and drug design [37]. The ACToR (Aggregated Com- atomic description of designed molecules, whose parameters
putational Toxicology Resource) database, that locates many have been optimized to minimize the damage done to
types and sources of data, has information about in vitro designing procedure. The YASARA energy function includes
bioassays and in vivo toxicology assays on chemical structure terms that have been found to be important for molecules
derived from more than 150 sources [34]. The admetSAR stability [39, 40, 43].
4 BioMed Research International

O O
OH
OH O O OH N N
O O
HO
HO OH O O O O
HO OH
O
O O
O O HO O N N O
HO O O OH HO O O
(a) Conduritol A (b) Conduritol B tetraacetate (c) Conduritol C cis- (d) Conduritol D (e) Conduritol E tetranitro
epoxide
OH
O OH
HO OH
O OH
HS HO O SH H
O OH HO O O H H OH
O
HO O OH
O HO O HO
O OH HO OH
HO S
O

HO OH O
(f) GS4 (g) Gymnemic acid I

HO OH OH
OH O OH

HO O OH O OH
H
H
O O OH
HO O

O O
HO O HO OH

HO O
(h) Gymnemic acid II (i) Gymnemoside A
OH
O OH

O OH
H
O H H OH
O

O HO OH
OH
O
O
(j) Gymnemoside B

Figure 2: Two-dimensional structures of the ten candidate drugs from Gymnema sylvestre.

2.5. Active Site Analysis. For the identification of the active protein and prepared as PDBQT files in AutoDock tools [45].
site and determination of pocket of the insulin receptor, To prepare for the ligand-protein interaction analysis, the
Computed Atlas of Surface Topography of proteins (CASTp) torsional bonds were set free from the ligands and saved
(http://sts.bioe.uic.edu/castp/calculation.php) server was used. as PDBQT file format. The prepared crystal structure of
This server provides an online resource for locating, delineat- 3LOH E was covered with grid box parameter for observing
ing, and measuring concave surface regions on three-dimen- its interaction with drug molecules. For this, a grid box
sional structures of proteins including pockets located on encompassing each ligand was set with the dimension (𝑋 =
protein surfaces and voids buried in the interior of proteins 98, 𝑌 = 98, and 𝑍 = 98) and center (𝑋 = 10.303, 𝑌 =
[44]. 107.879, and 𝑍 = 38.693) as well as grid box spacing 1.0 Å for
blind docking analysis. All the docking calculations were then
2.6. Molecular Docking Analysis. Before initiating the dock- performed with the set parameters by using AutoDock Vina
ing simulations, polar hydrogen was added to insulin receptor [46] which is an automated procedure for predicting the
BioMed Research International 5

O O
Br Br N
O O HO O
O O
HO OH O HO O
Br Br
O O HO

HO O O OH HO
(a) (b) (c) (d)

Figure 3: New designed analogues of Conduritol A (a), Conduritol B tetraacetate (b), Conduritol C cis-epoxide (c), and Conduritol D (d). To
increase their binding affinity, analogues have been generated by adding benzene, Br− , NO2 − , and O2 − into their 2D structures, respectively.

interaction of ligands with biomacromolecular targets. The

visualization of protein-ligand interaction was performed by
Pymol 1.1 [47] and Discovery studio 4.0 client. (a)

3. Results
(b)
3.1. Pharmacophore Study of Drug Compounds and Their
Analogues. The pharmacophore and QSAR properties of the
compounds were analyzed for their drug likeness, drug score,
toxicity, structural polarity, and oral bioavailability by using (c)
various software mentioned in Section 2 and the results are
listed in Tables 1 and 2. Among the ADMET properties,
human intestinal absorption is highest for Conduritol B
(d)
tetraacetate (0.9899 out of 1.0) while Caco-2 permeability is
highest for Gymnemic acid I and Gymnemoside A (0.9223 Figure 4: Energy minimization structure of designed molecules.
out of 1). All the other compounds show moderate to very Here red sticks designate the designed molecules. Designed ana-
high human intestinal absorption (0.5133–0.9691) as well as logues of Conduritol A (a), Conduritol B tetraacetate (b), Conduritol
Caco-2 permeability (0.5225–0.9040). No drug seems to cross C cis-epoxide (c), and Conduritol D (d).
the blood brain barrier as revealed by their score ranging
from 0.5000 to 0.9473. Unbound fraction of the drugs in
plasma is also very high (48–100%) except for Conduritol E
tetranitro (11%) implying their well distribution among the The four drugs showing good ligand and ADMET prop-
tissues. As expected, blood brain distribution of the drugs is erties but some toxic effects and lower binding affinity for
less than zero except Conduritol E tetranitro (0.33). Very high the insulin receptor have been considered for further analysis
metabolic score (>0.8000) was observed for all the ten candi- with an aim of identification of novel drug candidates. As a
date drugs. However, out of ten candidate drugs, Conduritol consequence, ten structural analogues for each of the four
A, Conduritol B tetraacetate, Conduritol C cis-epoxide, and drugs were generated and analyzed for pharmacophore and
Conduritol D showed mutagenic, reproductive, irritating, QSAR properties (Supplementary Figure S2, Table 3). Among
and tumorigenic effect, respectively (Table 1). Ligand prop- the 40 designed analogues, best one for each drug, namely,
erties were found in acceptable range for all the tested drugs Conduritol A with benzene, Conduritol B tetraacetate with
(Table 2). However, the six compounds possess better ligand Br− , Conduritol C cis-epoxide with NO2 − , and Conduri-
properties in contrast to the four drugs (Conduritols A–D) tol D with O2 − side chain (Figure 3), was selected based
showing toxicity. The six compounds require less docking on their pharmacophore and QSAR properties (Table 3).
energy (−8.0 to −10.9 Kcal/mol) compared to the four toxic Remarkably, the newly designed four analogues showed all
(−5.2 to −5.7 Kcal/mol) compounds. With broader polar the pharmacophore and QSAR properties within acceptable
surface area (220–401) six compounds show stronger inter- range. Before the docking energy analysis, YASARA program
actions to the target by donating two times more (7.7 versus was used in refining physical realism, stereochemistry, and
3.5 on average) and accepting three times more (14.7 versus side-chain accurateness in designed molecules. This program
4.75) hydrogen ion than that of the four toxic compounds. In yields the energy (START versus END) that ensures accuracy
addition to this, oral bioavailability of the six drugs is more of designed molecules (Figure 4). The energy compari-
than 70% with one exception of Gymnemic acid I (30–70%). son among designed molecules from the START energy
Furthermore, the six compounds are more likely to be used (66.1 KJ/mol, 720.2 KJ/mol, 705.5 KJ/mol, and 205.5 KJ/mol)
as drugs as revealed by their drug likeness and drug score. to END energy (−51.4 KJ/mol, 200.0 KJ/mol, −38.3 KJ/mol,
 6

Table 1: ADMET properties of Gymnema sylvestre compounds. Most data of ADMET properties were measured according to a measuring scale of 1.0.
Conduritol Conduritol B Conduritol C Conduritol Conduritol E Gymnemic Gymnemic Gymnemoside Gymnemoside
Properties GS4
A tetraacetate cis-epoxide D tetranitro acid I acid II A B
Absorption
Blood brain barrier 0.5000 0.9473 0.5337 0.5000 0.8859 0.5951 0.5396 0.5145 0.5396 0.5000
Human intestinal
0.9305 0.9899 0.6488 0.9305 0.9691 0.9375 0.5405 0.6906 0.5405 0.5133
absorption
Caco-2 permeability 0.5225 0.5742 0.6220 0.5225 0.5443 0.8205 0.9223 0.8955 0.9223 0.9040
Distribution
Blood brain distribution
−0.03 −0.01 −0.04 −0.03 0.33 −2.0 −0.48 −2 −0.46 −0.48
(LogBB)
Fraction unbound in
0.99 0.6 0.99 0.99 0.11 1 0.48 0.56 0.46 0.48
plasma
Volume of distribution
0.72 1.12 0.67 0.72 1.43 0.49 0.25 0.25 0.25 0.25
(𝑉𝑑 ) (L/kg)
Metabolism
CYP450 2C9 substrate 0.8335 0.8268 0.8081 0.8335 0.8564 0.8169 0.8585 0.8541 0.8585 0.8582
CYP450 2C9 inhibitor 0.8562 0.9772 0.9286 0.8562 0.7918 0.8666 0.8443 0.8549 0.8443 0.8346
Toxicity
Mutagenicity Yes No No No No No No No No No
Tumorigenicity No No No Yes No No No No No No
Irritating effects No No Yes No No No No No No No
Reproductive effects No Yes No No No No No No No No
BioMed Research International
 BioMed Research International

Table 2: Ligand properties of Gymnema sylvestre compounds.

Ligand Conduritol B Conduritol C Conduritol E Gymnemic Gymnemic Gymnemoside Gymnemoside
Conduritol A Conduritol D GS4
properties tetraacetate cis-epoxide tetranitro acid I acid II A B
Docking energy
−5.2 −5.7 −5.3 −5.6 −8.0 −8.7 −10.8 −9.4 −10.9 −10.4
(Kcal/mol)
Molecular
146.1412 314.28792 162.1406 146.1412 326.1314 714.78 806.98 682.838 806.9757 806.9757
weight (g/mol)
Number of H
4 2 4 4 2 14 7 9 7 7
donor
Number of H
4 8 5 2 12 21 14 12 14 14
acceptor
Log 𝑆 −1.958 −0.295 −0.237 −0.326 −4.065 −1.133 −1.133 −1.133 −5.38 −5.38
𝑐Log 𝑃 −1.63 0.31 −0.205 −1.631 −2.829 −5.169 −5.169 −5.169 −2.976 −2.976
TPSA 80.92 105.2 93.45 80.92 220.2 401 401 401 229.7 229.7
Drug likeness −0.05 −0.02 −0.218 −0.495 −2.168 −7.992 −7.992 −7.992 −6.524 −6.619
Oral More than More than More than
30%–70% 30%–70% 30%–70% 30%–70% 30%–70% More than 70% More than 70%
bioavailability 70% 70% 70%
7
8 BioMed Research International

Table 3: ADMET and QSAR properties of designed molecules.

Conduritol A Conduritol B tetraacetate Conduritol C epoxide

Ligand properties Conduritol D analogue
analogue analogue analogue
Cyclohex-5-ene-1,2,3,4- 5-Nitro-7- (5S,6S)-5,6-
3-Phenylcyclohex-5-
IUPAC name tetrayl oxabicyclo[4.1.0]heptane- Dihydroxycyclohex-3-ene-
ene-1,2,4-triol
tetracarbonobromidate 2,3,4-triol 1,2-dione
Docking energy −8.1 kcal/mol −7.8 kcal/mol −7.5 kcal/mol −8.0 kcal/mol
Molecular weight 206.24 573.77 191.14 142.11
Number of hydrogen bond
3 2 3 2
donors
Number of hydrogen bond
3 8 7 4
acceptors
Solubility −1.96 −5.87 −3.69 −0.43
TPSA 60.69 105.2 131.28 74.6
Number of rotatable bonds 1 8 1 1
Oral bioavailability More than 70% 30%–70% 30%–70% More than 70%
Absorption rate (Ka) min−1 0.022 0.054 0.0011 0.005
Volume of distribution (𝑉𝑑 )
1.28 1.47 0.36 0.65
(L/kg)
Violation 0 0 0 0
Toxicity No No No No
Drug likeness −1.01 −2.36 −2.29 −2.97
Val 377, Asn 407, Arg Val 377, Asn 407, Arg 409,
Val 377, Arg 409, Trp 414, Val 377, Asn 407, Arg 409,
409, Lys 433, Cys 435, Lys 433, Cys 435, Glu 438,
Lys 433, Cys 435, Ser 437, Lys 433, Cys 435, Glu 438,
Binding residues of Glu 438, Ala 466, Ser Lys 441, Gly 463, Ala 466,
Glu 438, Lys 441, His 440, Ala 466, ser 467, Glu 471,
3LOH E 467, Glu 471, leu 472, ser 467, Glu 471, leu 472,
Ala 466, Cys 468, Asn 470, leu 472, Gln 513, Lys 567,
Gln 513, Lys 567, and Pro 511, Gln 513, Asn 514,
and Gln 513, Tyr 579 and Lys 582
Lys 582 Lys 567, and Lys 582

and 58.6 KJ/mol) confirm the stability of the structural com- 3LOH E (Figure 6). The amino acid interactions of insulin
plexes of the designed molecules during the minimization receptor 3LOH E with these drugs were also identified (Fig-
of energy. The docking energy for the new analogues was ure 7). Amino acids that were unanimous to interact with at
found lower (−7.5 to −8.1 Kcal/mol) in comparison to their least five compounds were adopted as interacting amino acid.
parent compound (−5.2 to −5.7 Kcal/mol) as well as no toxic It was observed that Val 377, Arg 409, Lys 433, Cys 435, Glu
effect was associated with them. Finally, the four analogues 438, Glu 471, Leu 472, and Pro 511 exhibited strong binding
with improved drug likeness and drug score (Figure 5) also interactions with the six docked compounds (Figure 7).
claimed their position in the queue of the novel antidiabetic Among these, Val 377, Glu 438, and Leu 472 were common
drugs. in interactions between IR protein and all the six drugs. The
interactions that play significant role in the determination
3.2. Active Site and Molecular Docking Analysis. The active of binding energy and stability of these receptor-ligand
site area of the insulin receptor protein and the number of complexes were recognized as hydrogen bond and hydropho-
amino acid residues involved in it were determined with bic and electrostatic interactions. Evidently, all of the nine
the CASTp server. This provides a significant insight of the interacting amino acids are located in the active site pocket
docking simulation study to locate the active site cleft and
of the insulin receptor protein (Supplementary Figure S3).
the amino acid residues that interact with different ligands.
Besides these drugs, the docking results of the structural
The preeminent active site is found with 5311.9 area and a vol-
analogues of the remaining four drugs confirmed their strong
ume of 40219 amino acids (Supplementary Figure S3). The
molecular docking analysis performed with AutoDock Vina interactions with the insulin receptor protein (Figure 8). Val
for the six candidate drugs showing good pharmacophore 377, Arg 409, Lys 433, Cys 435, Glu 438, Ala 466, Ser 467,
and QSAR properties revealed variations in their binding Glu 471, and Leu 472 were found in binding interactions with
energies. AutoDock Vina produced nine possible binding the four designed analogues (Figure 8). But Val 377, Lys 433,
positions as output for each drug. Out of nine possible ligands Cys 435, Glu 438, and Ala 466 were common in interactions
binding positions the best one was chosen for each compound with all designed drugs and 3LOH E. Interestingly, these
based on the lowest docking energy. The results pointed out amino acids are also in the active site pocket of the insulin
that all the six compounds efficiently bind to insulin receptor receptor protein (Supplementary Figure S3). These amino
BioMed Research International 9

1
0.9
0.8
0.7 0.61 0.61

Drug score
0.6 0.52
0.5 0.447
0.4
0.3 0.265 0.265 0.265
0.21
0.2
0.101 0.101
0.1
0

GS4

Gymnemic acid I

Gymnemic acid II

Gymnemoside A

Gymnemoside B
Con. E tetranitro

Con. A analogue

Con. D analogue
Con. B tetraacetate analogue

Con. C epoxide analogue

Figure 5: Computational drug score of suggested drug molecules. Here blue color indicates the medicinal plant derived drug compounds
and orange color indicates the designed analogue drug compounds.

Interacting cleft

Interacting drugs

(a)

(b)

Figure 6: Docking simulation of six compounds of Gymnema sylvestre with E chain of 3LOH. (a) Ribbon structure of 3LOH E showed the
binding affinity of all six drugs to the E chain. (b) Space filling model also showed the six drugs in active site cleft of E chain.

acid residues identified a binding site within the E chain of site (Figure 9). It is therefore to predict that amino acid
3LOH by blind docking analysis (Supplementary Figure S4). residues Val 377 and Glu 438 could play a crucial role for both
Interacting amino acids with docking analysis confirmed that plant derived drug compounds and designed drug molecules
all the drug molecules for this study bind in the same binding in mimicking the insulin activity.
10 BioMed Research International

Color (dot) (Interactions type) Color (dot) (Interactions type) Color (dot) (Interactions type)
Yellow Hydrogen bond Yellow Hydrogen bond Yellow Hydrogen bond
Red Electrostatic Red Electrostatic Red Electrostatic
Blue Hydrophobic Blue Hydrophobic Blue Hydrophobic
(a) (b) (c)

Color (dot) (Interactions type) Color (dot) (Interactions type) Color (dot) (Interactions type)
Yellow Hydrogen bond Yellow Hydrogen bond Yellow Hydrogen bond
Red Electrostatic Red Electrostatic Red Electrostatic
Blue Hydrophobic Blue Hydrophobic Blue Hydrophobic
(d) (e) (f)

Figure 7: Interaction between drugs (a–f) and active site amino acid residues of 3LOH E. (a) Conduritol E tetranitro, (b) GS4, (c) Gymnemic
acid I, (d) Gymnemic acid II, (e) Gymnemoside A, and (f) Gymnemoside B. Red stick represents the drug compounds. Yellow dots represent
the hydrogen bond interaction. Red dots represent the electrostatic interactions and blue dot also represents the hydrophobic interactions
with amino acid residues. The common interactions with amino acid residues among the six compounds are Val 377, Glu 438, and Leu 472.

4. Discussion abundant in South Asia to study them as potent antidiabetic

drugs (Figure 2). The target for the current study is insulin
Compounds screening leading to drug design have been an receptor protein “3LOH” of which 3D crystal structure is
active area of research for many years. Due to the wearisome available with ligands. To prepare the target for the screening
and expensive nature of investigational screening procedures, of drug compounds, we removed the ligands and chains (A, B,
computational compound screening has been pursued exten- C, and D) and kept only E chain of the 3LOH crystal structure
sively in recent years [48, 49]. The endeavor of this study was (Supplementary Figure S1). Blind docking analysis for the
based on the relationship between drug-receptor interactions whole 3LOH E protein with the candidate drugs discloses
and its in silico analysis for designing, identifying, and evalua- their (drugs) highest affinity towards the active site cleft
ting novel drugs against diabetes mellitus. The new drug can- amino acid residues of the 3LOH E chain (Supplementary
didates were identified from the medicinal plant G. sylvestre Figure S3). Henceforth, the drugs affinity towards IR protein’s
BioMed Research International 11

(a)

(A) (B)

Color (dot) (Interaction types) Color (dot) (Interaction types)

Yellow Hydrogen bond Yellow Hydrogen bond
Red Electrostatic Red Electrostatic
Gray Hydrophobic Gray Hydrophobic

(C) (D)
(b)

Figure 8: Interaction between the four novel designed molecules and active site amino acid residues of 3LOH E. (a) Space filling model
of 3LOH E with four novel designed molecules in the active site cleft of E chain. (b) Designed drug compounds interactions with amino
acid residues of insulin receptor chain E. (A) Conduritol A analogue, (B) Conduritol B tetraacetate analogue, (C) Conduritol C cis-epoxide
analogue, and (D) Conduritol D analogue. Here, marine sticks designate the drug compounds. The interactions with most common amino
acid residues of these novel molecules are Val 377, Lys 433, Cys 435, Glu 438, and Ala 466.

active site could be shown which is the most desired binding license-agreed software. The pharmacokinetics and pharma-
sites for the suggested drug candidates (Supplementary Fig- cology for absorption, distribution, metabolism, elimination,
ure S4). and toxicity are assessed by the ADMET properties that
The pharmacophore properties of the selected molecules describe the disposition of a drug-like compound within the
were carried out by using the up-to-date online-based and body of an organism [50]. All the candidate drugs tested in
12 BioMed Research International

toxicity of these designed molecules and hence allow them

to be the probable antidiabetic drug candidates (Table 3).
The docking study of these novel compounds identifies their
higher binding affinity to their target insulin receptor. Inter-
actions of the native plant derived compounds as well as four
analogues are exerted in the active site amino acid of the IR
(Figures 6, 7, and 8). The interactions that play significant role
in the determination of binding energy and stability of these
receptor-ligand complexes were recognized as hydrogen
bond and hydrophobic and electrostatic interactions. This
interaction of these drugs confirm their insulin mimicking
properties. Considering all these facts, it might be assumed
that these drugs will activate IR and facilitate translocation
of glucose transporter 4 (Glut-4) to the plasma membrane
and influx of glucose and thereby help maintain normal blood
glucose level [15]. Therefore, all the six drug compounds espe-
cially Gymnemoside A, B and Gymnemic acid I, II together
with four designed drug molecules might be proposed as oral
Figure 9: Drugs (natural plant compounds and designed molecules) drugs after experimental validation against diabetes mellitus.
binding into the binding site of 3LOH E chain. Val 377 and Glu 438
This in silico analysis supported the potentials of tested
were the common binding residues among these drug compounds.
antihyperglycemic natural compounds (Gymnemoside B and
GS4) as oral drugs [24, 25]. Along with this, this study ascer-
tained the potentials of nonconfirmed antihyperglycemic
natural compounds (Gymnemoside A, Conduritol E tetrani-
this study show moderate to high absorption rate. Impor- tro, Gymnemic acid I, and Gymnemic acid II) as oral drugs.
tantly no drug seems to cross blood brain barrier. High Finally, this study proposes four novel drugs for their
distribution of the drugs in plasma indicates their availabil- experimental validation as potential oral antidiabetic drug
ity in all tissues. However, no blood brain distribution is (Figure 3).
observed. Metabolism of all the drugs is shown to be perfect. The current study shed light into the interactions between
With no toxicity six drugs, namely, Conduritol E tetranitro, 3D structure of insulin receptor active site and predicted drug
GS4, Gymnemic acid I, Gymnemic acid II, Gymnemoside molecules. All the pharmacophore analysis including molec-
A, and Gymnemoside B show characteristics suitable as drug ular docking of candidate drug molecules reveals their high
(Table 1). affinity to the IR active site amino acids and their eligibility
Investigational analysis revealed that the putative com- as bioavailable oral drugs. Though these in silico analyses
pounds (Figure 2) used in the present analysis have signif- predicted ideal antidiabetic drugs it is limited by the lack of
icant values to diabetes mellitus. All the ten selected drug experimental validations. In addition to this, no comparison
compounds were analyzed on the basis of binding energy studies among the candidate drugs as well as candidate
values to insulin receptor and their drug properties (Table 2). drugs with known antidiabetic drugs have been performed.
After docking study, all six compounds with no toxic effects Nevertheless, the results of this study provide opportunities
showed their high binding affinity to the E chain of the insulin for further evaluation of the proposed drugs in vitro and
receptor protein (Figure 6). Gymnemoside A and Gymnemo- in vivo for establishing their candidature as alternative oral
side B were interacted with the highest number (21) of amino drugs for the treatment of diabetes.
acids. Although GS4 possess the ability to interact with its
target having the highest number of hydrogen donors as
well as acceptor, the highest binding energy was observed in 5. Conclusion
Gymnemoside A (−10.9 Kcal/mol). It is clearly apparent that
Conduritol E tetranitro, GS4, Gymnemic acid I, Gymnemic Prolonged usage of insulin often leads to insulin insensitivity
acid II, Gymnemoside A, and Gymnemoside B might be and insulin resistance of the cell as well as other daunting
suggested as potent antidiabetic drug candidates because of side effects such as the risk of hypoglycemia. Moreover, the
having lowest docking energy indicating their higher binding complications and pain associated with the administration
affinity to the insulin receptor protein. To impart this study of insulin cannot also be denied. Taking these complications
towards availability and improvement of antidiabetic drugs, into consideration, in this present study, using computational
the four compounds, namely, Conduritol A, Conduritol B and bioinformatics tools we have identified, designed, and
tetraacetate, Conduritol C cis-epoxide, and Conduritol D proposed ten oral based novel therapeutic drugs for the
showing lower binding affinity to insulin receptor and toxic treatment of diabetes mellitus which might help reduce our
effects were employed to add benzene, Br− , NO2 − , and O2 − in dependency on insulin without causing considerable side
their structure to generate novel compounds and to increase effects and associated pain during administration. Further
their antidiabetic potentiality (Figure 3). The pharmacophore wet lab assessment of these drugs has to be performed to
and the QSAR analysis suggest that there is no indication of establish their insulin mimicking activity.
BioMed Research International 13

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