Design, synthesis and docking study of 5-(substituted benzylidene) thiazolidine-2,4-dione derivatives as inhibitors of protein tyrosine phosphatase 1B

Article abstract of DOI:10.1016/j.bmcl.2014.05.099

A series of novel 5-(substituted benzylidene)thiazolidine-2,4-dione derivatives was designed, and synthesized based on our previous studies. Also their activities were evaluated as competitive inhibitors of protein tyrosine phosphatase 1B (PTP1B). Compounds 6d-6g, 7b, 7c, 7e, 7j, 7k, 7m, 14b and 14e-14f showed potent inhibitory effects against PTP1B, and compound 7e, the most potent among the series, had an IC₅₀ of 4.6 μM. Also a Surflex-Dock docking model of 7e was studied. Compound 7e showed a negative binding energy of -7.35 kcal/mol and a high affinity to PTP1B residues (Gly220, Ala217, Arg221, Asp181, Ser216, Cys215, Phe182, Gln262 and Ile219) in the active sites, indicating that it may stabilize the open form and generate tighter binding to the catalytic sites of PTP1B.

Full text of DOI:10.1016/j.bmcl.2014.05.099

Accepted Manuscript
Design, Synthesis and Docking Study of 5-(Substituted Benzylidene)Thiazoli-
dine-2,4-dione Derivatives as Inhibitors of Protein Tyrosine Phosphatase 1B
Zengtao Wang, Zhiguo Liu, Woojung Lee, Su-Nam Kim, Goo Yoon, Seung
Hoon Cheon
PII:
S0960-894X(14)00608-8
DOI:
http://dx.doi.org/10.1016/j.bmcl.2014.05.099
BMCL 21713
Reference:
Bioorganic & Medicinal Chemistry Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
16 April 2014
26 May 2014
29 May 2014
Please cite this article as: Wang, Z., Liu, Z., Lee, W., Kim, S-N., Yoon, G., Cheon, S.H., Design, Synthesis and
Docking Study of 5-(Substituted Benzylidene)Thiazolidine-2,4-dione Derivatives as Inhibitors of Protein Tyrosine
Phosphatase 1B, Bioorganic & Medicinal Chemistry Letters (2014), doi: http://dx.doi.org/10.1016/j.bmcl.
2014.05.099
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Design, Synthesis and Docking Study of 5-(Substituted
Benzylidene)Thiazolidine-2,4-dione Derivatives as Inhibitors of Protein
Tyrosine Phosphatase 1B
Zengtao Wanga, Zhiguo Liub, Woojung Lee c, Su-Nam Kimc, Goo Yoond, and Seung Hoon Cheon a, ∗
a College of Pharmacy and Research Institute of Drug Development, Chonnam National University; Gwangju 500-757, Korea
b School of Pharmacy, Wenzhou Medical College, 1210 University Town, Wenzhou, Zhejiang 325035, China, and Wenzhou
Undersun Biotechnology Co., Ltd., Wenzhou, Zhejiang, China
c KIST Gangneung Institute, Gangneung 210-340, Korea
d College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Jeonnam 534-729, Korea.
*Corresponding author shcheon@chonnam.ac.kr, Tel: +82625302929, Fax: +82625302911
Abstract
A series of novel 5-(substituted benzylidene)thiazolidine-2,4-dione derivatives was designed, and
synthesized based on our previous studies. Also their activities were evaluated as competitive
inhibitors of protein tyrosine phosphatase 1B (PTP1B). Compounds 6d-6g, 7b, 7c, 7e, 7j, 7k, 7m,
14b and 14e-14f showed potent inhibitory effects against PTP1B, and compound 7e, the most potent
among the series, had an IC50 of 4.6 µM. Also a Surflex-Dock docking model of 7e was studied.
Compound 7e showed a negative binding energy of -7.35 kcal/mol and a high affinity to PTP1B
residues (Gly220, Ala217, Arg221, Asp181, Ser216, Cys215, Phe182, Gln262 and Ile219) in the
active sites, indicating that it may stabilize the open form and generate tighter binding to the catalytic
sites of PTP1B.
Key words: thiazolidinediones, PTP1B, synthesis, docking study
The term diabetes mellitus (DM) is used to simply describe a heterogeneous group of metabolic
disorders characterized by chronic hyperglycemia with disturbances of carbohydrate, fat and protein
metabolism.1 It is often accompanied by characteristic long-term complications such as retinopathy,
nephropathy and neuropathy.2 DM is more prevalent than ever, particularly in developing countries.
More than 285 million people suffer from DM and this number is expected to rise to 439 million
cases by 2030.3 The most common form of DM is type 2, accounting for 90 to 95 percent of all
diabetes cases, which is characterized by combining insulin resistance and lacking compensatory
∗ Corresponding author. Tel.: +82-62-530-2929; fax: +82-62-530-2911; e-mail: shcheon@chonnam.ac.kr

response to sufficiently create insulin, resulting from a failure of pancreatic islet β-cells.4,5 In
addition, the prevalence of type 2 diabetes mellitus (T2DM) is escalating, mainly due to the rapidly
increasing incidence of overweight and obesity. More than 80 percent of people with T2DM show
overweight and it has become a recognized risk factor for T2DM.6-8 More importantly, T2DM is a
leading cause of early death, heart disease, stroke, kidney disease and blindness.9
These warning events present grave threats to our health and quality of life and have incited a
search for pharmacological agents capable of inhibiting the negative regulators of the insulin
signaling pathways and/or potentiating the action of insulin. Mounting data from cellular,
biochemical, mouse and human genetic and chemical inhibitor studies have strongly implicated
protein tyrosine phosphatase 1B (PTP1B) as a key negative regulator of both, insulin and leptin
signaling. PTP1B knockout mice exhibited improved insulin sensitivity with reduced plasma glucose
and insulin levels.10,11 Furthermore, these mice have lower adiposity and are resistant to weight gain.
Thus, these studies provided a strong insight into developing inhibitors of PTP1B to treat diabetes
and obesity.
We have been searching for a lead compound from natural products as a potential preclinical
candidate to treat T2DM for the past few years and reported that licochalcone A and licochalcone E
showed good PTP1B inhibitory activities.12 In addition, the results of structure–activity relationship
study of retrochalcones related to licochalcone E have been reported recently.13 With our continuing
interests in retrochalcones, the introduction of thiazolidinedione ring instead of a benzoyl group in
retrochalcones, gave compounds with potent inhibitory activities (Figure 1). For example, compound
6b showed IC50 value of 11.3 µM. Although some PTP1B inhibitors containing thiazolidine group
have been reported,14-16 most of them incorporate a large aromatic substituent or charged phosphor
tyrosine (pTyr) mimetic group such as phosphonates, carboxylic acids and sulfamic acids which have
proven a lack of cell membrane permeability and oral bioavailability because of the strong negative
charge carried by the pTyr mimetics as well as their high molecular weight.17 The nature of the
highly charged active site and the relatively shallow of the surrounding protein surface of PTP1B
provide a great challenge to medicinal chemists for the discovery of cell permeable and orally bio-
available PTP1B inhibitors. Hence, there is an urgent need to develop small molecule PTP1B
inhibitors devoid of any charged moieties and with good inhibitory activities that can combat T2DM.

Figure 1. Structures of licochalcone E and 6b
Herein we report the results of synthesis, PTP1B inhibitory activities, structure-activity
relationship (SAR) and docking study of 5-(substituted benzylidene)thiazolidine-2,4-dione
derivatives as a part of our efforts to discover novel non-charged small molecule PTP1B.
The synthesis of compounds 6a-6g and 7a-7m from 2,4-dihydroxybenzaldehyde 1 was carried
out following the procedure depicted in Scheme 1. The bromination of 1 followed by selective MOM
protection of 4-hydroxyl group provided compound 3b, then methylated with MeI/K2CO3,
deprotected with concentrated hydrochloric acid in methanol to form the aldehyde 4b, which in turn
reacted with correspond halides to afford intermediates 5a-5e. The selective MOM protection of 4-
phenol in compound 1 and then the methylation of 2-phenol with methyl iodide followed by acid
hydrolysis of MOM yielded the compound 4a. Compounds 6a-6g were synthesized using
Knoevenagel condensation with 2,4-thiazolidinedione and suitable benzaldehydes (4a, 5a-5e) in
refluxing toluene in the presence of piperidinium acetate.18 The proper substitution at the nitrogen
atom of the thiazolidinedione ring of 6b-6g gave compounds 7a-7m.
Scheme 1. Reagents and Conditions: (a) Br2, acetic acid, rt, 84%; (b) MOMCl, K2CO3, acetone, rt,
86%; (c) CH3I, K2CO3, acetone, rt, 16 h; 6N-HCl, rt, 95%; (d) R1X, K2CO3, acetone, rt, 61-91%; (e)
thiazolidine-2,4-dione, piperidinium acetate, toluene, reflux, 59-86%; (f) R2X, K2CO3, acetone,
reflux, 60-91%.

The synthesis of compounds 13a-13f and 14a-14g was carried out following the procedure
depicted in Scheme 2. O-Allylphenol 10 was readily prepared in a three-step sequence from allyl
bromide and 2,4-dihydroxybenzaldehyde via allylation of phenol 1 followed by methylation to 9 and
subsequent Claisen rearrangement. Compound 12 was obtained via Knoevenagel condensation of the
commercially available 2,4-thiazolidinedione and the aldehyde 11. Treatment of 12 with suitable
alkyl halides in the presence of potassium carbonate afforded compounds 13a-13f. The removal of
the THP under acidic conditions finally gave the compounds 14a-14g.
Scheme 2. Reagent and Conditions: (a) Allyl bromide, K2CO3, acetone, rt, 79%; (b) CH3I, NaI,
K2CO3, acetone, rt, 90%; (c) 200oC, 24 hours, 39%; (d) 3,4-Dihydro-2H-pyran, PPTS, CH2Cl2, rt,
75%; (e) Thiazolidine-2,4-dione, piperidinium acetate, toluene, reflux, 78%; (f) R2X, K2CO3, acetone,
reflux, 62-89%; (g) 6N-HCl, rt, 37-65%.
The introduction of 5-arylidene moiety provided only Z isomers, as already demonstrated by X-
ray diffraction studies.19,20 The 1H NMR spectra showed only one signal attributable to the resonance
of the 5-methylidene proton in the range 7.81-8.24 ppm. In their 13C NMR spectra, the 5-
methylidene carbon and C5 of the thiazolidinedione ring resonated in the ranges 131.94-139.04 and
116.12-122.39 ppm, respectively. Spectroscopic data (1H, 13C NMR and IR) confirmed the structures
assigned to compounds 6-7 and 12-14.
Table1：Structures and inhibition of PTP1B of thiazolidinedione derivatives 6a-14g a
Comp.
R1
H
R2
H
H
H
H
R3 IC50 (µM)a
Comp.
R1
Bu
R2
Bu
Bn
H
R3
Br
IC50 (µM)b
6a
H
7l
29.8
11.3
14.2
8.1
>30
6.6
6b
H
Br
Br
Br
7m
Bu
Br
6c
Me
Allyl
12
THP
THP
Allyl
Allyl
12.2
>30
6d
13a
Me

6e
6f
Prenyl
Bu
H
H
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
13b
13c
13d
13e
13f
14a
14b
14c
14d
14e
14f
14g
THP
THP
THP
THP
THP
H
Isopropyl Allyl
5.3
4.9
>30
>30
22.7
20.6
>30
>30
6.4
Allyl
Prenyl
Bu
Allyl
Allyl
Allyl
Allyl
Allyl
6g
7a
7b
7c
7d
7e
7f
Bn
H
7.6
Me
Me
22.3
8.1
Bn
Me
Bn
Prenyl
Prenyl
Prenyl
Prenyl
Prenyl
Prenyl
Bu
Me
Me
8.2
Allyl
Isopropyl
Bu
H
Isopropyl Allyl
17.0
4.6
H
Allyl
Prenyl
Bu
Allyl
Allyl
Allyl
Allyl
Allyl
>30
12.0
9.6
H
12.3
10.0
10.3
12.1
7.9
7g
7h
7i
Prenyl
Bn
H
H
Bn
7.2
Me
H
H
29.3
4.0
Ursolic acidc
7j
Bu
Allyl
7k
Bu
Isopropyl
9.7
a General formula of the target compounds in figure 1.
b Results are expressed as IC50 values (µM).
c Positive control.
The synthesized 5-(substituted benzylidene)thiazolidine-2,4-dione derivatives (6a-6g, 7a-7m,
12，13a-13g and 14a-14g) were evaluated as inhibitors against PTP1B using p-nitrophenyl
phosphate (pNPP) as a substrate and the results are summarized in Table 1.21 The known PTP1B
inhibitor, ursolic acid (IC50 = 4.0 µM), was used as positive control. Compounds 6d-6g, 7b, 7c, 7e, 7j,
7k, 7m, 14b and 14e-14f were proven to be highly active PTP1B inhibitors with IC50 values from 4.6
to 9.7 µM, while compounds 6b, 6c, 7d, 7g-7i, 12 and 14d showed moderate activity with IC50
values from 10.0 to 17.0 µM. When R3 was bromine, compounds with allyl, prenyl, n-butyl or benzyl
as R1 and hydrogen as R2 showed excellent activity. But the most active compound had prenyl as R1,
isopropyl as R2, and bromine as R3. In general, compounds have lower activity with allyl rather than
bromine as R3 Though, compounds displayed excellent activity with hydrogen as R1, either
.
isopropyl, n-butyl or benzyl as R2 and allyl as R3 These results indicate that steric factors play
.
important role in binding as shown in molecular modeling study (vide infra).
The crystallographic 3D structural information of the biomolecular targets offer tremendous
opportunities for establishing novel drug design strategies to accelerate the drug discovery process.
Available X-ray crystallographic data on Protein Data Bank facilitated the performance of virtual
structure based drug discovery projects aiming at PTP1B as a molecular target for type 2 diabetes. In
this regard, docking simulation plays a key role in the structural molecular biology and computer-
assisted drug design. Binding models for receptors and ligands via a lowest energy pathway may be
best represented by docking simulations. One of the most effective docking techniques is Surflex-
Dock.22 The literature review shows that Surflex-Dock has offered several fruitful advantages in the
field of drug design.23 The binding model of compound 7e and PTP1B (PDB ID: 2QBS) is

depicted in Figure 2. The thiazolidinedione group occupies the large hydrophobic pocket directed
toward Gly220, Ala217, Asp181 and Phe182. Specifically, the carbonyl group at the
thiazolidinedione ring interacts with Gly220 of the PTP1B domain via the formation of a strong
hydrogen bond (hydrogen bond distance is 2.88 Å). This would help to stabilize the open form and
generate tighter binding to the catalytic sites of PTP1B. Furthermore, the interactions were also
stabilized by the hydrophobic residues of the inner cavity, such as Ala217, Arg221, Asp181, Ser216,
Cys215, Phe182, Gln262 and Ile219 as the active pocket consisted of 10 amino acid residues in
Figure 2.
Figure 2. Binding mode of 7e with active sites of PTP1B (2QBS). The right green coloring of
residues indicates neighboring subunits that form the binding pocket for 7e. The side chain atoms are
colored as follows: carbon green, nitrogen blue, oxygen red and hydrogen gray. The 7e atoms are
colored as follows: nitrogen blue, oxygen red, carbon yellow and sulfur orange.
In the present work, we have designed and synthesized a series of 5-(substituted
benzylidene)thiazolidine-2,4-dione derivatives as potent PTP1B inhibitors. Compounds 6d-6g, 7b,
7c, 7e, 7j, 7k, 7m, 14b and 14e-14f showed potent inhibitory activities with IC50 values ranging from
4.6 to 9.7 µM. In particular, compound 7e as the most potent of the present series had an IC50 of 4.6
µM with bromine at C-5 and O-prenyl group at C-4 position of the benzene ring and isopropyl group
at the nitrogen of the thiazolidinedione ring. Compound 7e showed negative binding energy of -7.35
kcal/mol and a high affinity to PTP1B residues (Gly220, Ala217, Arg221, Asp181, Ser216, Cys215,
Phe182, Gln262 and Ile219) in the active sites, indicating that it may stabilize the open form and
generate tighter binding to the catalytic sites of PTP1B.
Acknowledgments
This research was supported by Basic Research Program through the National Research Foundation
of Korea (NRF) funded by the Ministry of Education (grant No. 2012R1A1A2006613). We thank the

Korea Basic Science Institute (KBSI), Gwangju branch, for performing the NMR and HRMS
experiments.
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Graphical Abstract
Design, Synthesis and Docking Study of 5-(Substituted
Benzylidene)Thiazolidine-2,4-dione Derivatives as Inhibitors of
Protein Tyrosine Phosphatase 1B
Leave this area blank for abstract info.
Zengtao Wanga, Zhiguo Liub, Woojung Lee c, Su-Nam Kimc Goo Yoon3, and Seung Hoon Cheona, ∗