Sulfonamide derivatives containing dihydropyrazole moieties selectively and potently inhibit MMP-2/MMP-9: Design, synthesis, inhibitory activity and 3D-QSAR analysis

Article abstract of DOI:10.1016/j.bmcl.2015.08.026

New series of sulfonamide derivatives containing a dihydropyrazole moieties inhibitors of MMP-2/MMP-9 were discovered using structure-based drug design. Synthesis, antitumor activity, structure-activity relationship and optimization of physicochemical pro

Full text of DOI:10.1016/j.bmcl.2015.08.026

Bioorganic & Medicinal Chemistry Letters xxx (2015) xxx–xxx
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Sulfonamide derivatives containing dihydropyrazole moieties
selectively and potently inhibit MMP-2/MMP-9: Design, synthesis,
inhibitory activity and 3D-QSAR analysis
Xiao-Qiang Yan y, Zhong-Chang Wang y, , Zhen Li, Peng-Fei Wang, Han-Yue Qiu, Long-Wang Chen,
⇑
⇑
⇑
Xiao-Yuan Lu, Peng-Cheng Lv , Hai-Liang Zhu
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, People’s Republic of China
a r t i c l e i n f o
a b s t r a c t
Article history:
New series of sulfonamide derivatives containing a dihydropyrazole moieties inhibitors of MMP-2/MMP-
9 were discovered using structure-based drug design. Synthesis, antitumor activity, structure–activity
relationship and optimization of physicochemical properties were described. In vitro the bioassay results
revealed that most target compounds showed potent inhibitory activity in the enzymatic and cellular
assays. Among the compounds, compound 3i exhibited the most potent inhibitory activity with IC50 val-
Received 5 March 2015
Revised 22 July 2015
Accepted 10 August 2015
Available online xxxx
ues of 0.21
compound CMT-1 (1.26
l
M inhibiting MMP-2 and 1.87
lM inhibiting MMP-9, comparable to the control positive
Keywords:
Sulfonamide derivatives
Anticancer
MMP-2/MMP-9
Docking
3D-QSAR
l
M, 2.52 M). Docking simulation was performed to position compound 3i into
l
the MMP-2 active site to determine the probable binding pose. Docking simulation was further per-
formed to position compound 3i into the MMP-2 active site to determine the probable binding model
the 3D-QSAR models were built for reasonable design of MMP-2/MMP-9 inhibitors at present and in
future.
Ó 2015 Elsevier Ltd. All rights reserved.
Matrix metalloproteinases (MMPs) are a family of zinc- and
calcium-dependent endopeptidases that are capable of degrading
and remodeling of connective tissues.1,2 Their key roles in physi-
ological tissue remodeling and repair of the extracellular matrix
have attracted considerable attention in development of drugs
with a potential for therapeutic applications in a variety of
diseases including arthritis,3,4 tumor growth and metastasis,5
periodontal disease,6 multiple sclerosis,7 and congestive heart fail-
ure.8,9 These diseases are associated with dysregulated MMP
expression and activation. Under normal physiological conditions,
activated MMPs are tightly controlled by maintaining a balance
between the synthesis of the active forms and their inhibitions
by tissue inhibitors of matrix metalloproteinases (TIMPs). The
endogenous tissue inhibitors of MMPs could serve as effective
anticancer agents.10,11 In addition to other direct TIMP/MMP
interactions, the TIMPs also bind to the zinc atom of the active site
of the MMPs to block their activity because of containing a Zn2+
ion in the catalytic domain.12,13 Therefore, inhibiting MMPs is an
attractive approach which could treat multitudes of diseases. For
example, many inhibitors of MMP-2/MMP-9 have proved to
prevent cancer tumor growth.14 In the joint efforts of a number
of laboratories working in the field, many potent and orally
active broad-spectrum MMP inhibitors were discovered during
the past decade, some of which had reached an advanced
clinical trial. Representative examples include 1–8 had been
tested against cancers,11,15–17 moreover, MMP inhibitors
9
(cipemastat)18 and 10 (illomastat)19 were tried in the clinics for
inflammation.
⇑
Corresponding authors. Tel./fax: +86 25 83592672.
E-mail address: zhuhl@nju.edu.cn (H.-L. Zhu).
These two authors equally contributed to this paper.
y
http://dx.doi.org/10.1016/j.bmcl.2015.08.026
0960-894X/Ó 2015 Elsevier Ltd. All rights reserved.
Please cite this article in press as: Yan, X.-Q.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.026

2
X.-Q. Yan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
O
O
H
N
HO
O
O
NH
N
N
H
NHMe
H
N
O
O
HO
S
O
N
H
N
H
S
O
N
H
N
H
OH
O
2 marimastat (BB-2516)
1 PNU-141803
3 BB-1101
H2N
NH
H2N
O
H
N
N
O
H
N
O
HN
S
O
S
N
O
O
O
O
N
O
N
S
O
NH
HN
5
O
H
N
4
NH2
O
O
N
H
NH
O
N
O
O
O
O
N
H
N
N
O
N
H
N
H
S
SH
O
NH2
7
6 BMS-275291
O
HO
N
H
N
O
O
S
N
O
O
O O
O
N
N
HO
HN
O
N
H
O
NH
OH
O
N
NH
S
NH
8 prinomastat (AG-3340)
9 cipemastat (Ro 32-3555)
10 illomastat (GM-6001)
In the last twenty years, scientists in both academia and industry
MMP-2/MMP-9, utilizing dihydropyrazole and sulfonamide as
new structural classes.
had carried out an industry-wide effort to seek selective MMP inhi-
bitors as innovative medicines.20,21 Unfortunately, there had been
no clinically useful inhibitor to be demonstrated until now. In gen-
eral, the major reasons for the failure of these trials were non-speci-
ficity, nonselective toxicity and dose-limiting efficacy.21 To
overcome these present difficulties, we undertook additional efforts
to discover the new chelating groups toward the MMP zinc ion,22,23
including secondary amine, amide, imine, imidazole, carboxylate,
aminocarboxylate, sulfhydryl, hydroxamate, phosphonateand phos-
phinate moiety and sulfonamides.24–29 Sulfonamides had been
selected as pharmacological agents due to their biological activities
and their potential applications. The application of sulfonamides
was widespread due to its anticancer30 and antibacterial.31 It
recently reported that a series of structurally novel dihydropyrazole
derivatives containing the class of primary sulfonamides
(RSO2NH2), sulfamates (ROSO2NH2), and sulfamides (RNHSO2NH2)
at the p-position of the phenyl ring showed substantial antitumor
activity, both in vitro and in vivo. Some of these derivatives had
been in clinical trials, and there was much optimism that it might
contribute to guide novel alternative anticancer drugs, devoid of
the side effects of the present available pharmacological agents.32,33
Furthermore, special attention had been placed lately on the use of
pyrazole for anticancer. Recently, a series of novel pyrazole deriva-
tives were discovered as potent anticancer agents in our group, and
some of them had demonstrated potent antitumor activity.34,35
In the preceding work, we have reported the good inhibitory to
MMP-2 of a series of benzosulfonamide benzenesulfonates as a
part of our studies on the design and synthesis of MMPs
inhibitors.36 Here we extend the earlier work of benzosulfonamide
incorporating benzenesulfonate moieties, and describe the struc-
ture-based design and synthesis of novel and potent inhibitors of
The 25 novel sulfonamide derivatives containing dihydropyra-
zole moieties, as MMP-2/MMP-9 inhibitors (3a–3y), were herein
synthesized by following the synthetic pathway depicted in
Scheme 1. The starting diverse substituted chalcones (2a–2y) were
synthesized by the substituted acetophenone and equivalent naph-
thaldehyde in the presence of excess sodium hydroxide, using 40%
potassium hydroxide as catalyst in ethanol. Then added acetic acid
as acid-binding agent, the cyclization reaction of different chal-
cones and 4-sulfamoylphenyl hydrazine hydrochloride was in
refluxing ethanol for 5–7 h, monitored by thin layer chromatogra-
phy (TLC). The crude products were purified in good yields, by
recrystallization with ethanol, ethyl acetate and acetone
(1:1:0.05). All of the target compounds gave satisfactory analytical
and spectroscopic data 1H NMR, EI-MS, which were in accordance
with their depicted structures. Furthermore, the crystal structures
of compounds 3j, 3m and 3s were determined by single crystal X-
ray diffraction analysis in Figure 1 and Table 1.
In the present work, twenty-five of the newly synthesized
derivatives (3a–3y) were evaluated for their in vitro growth inhibi-
tory activities of four cultured cell lines, which were A549, HeLa,
MCF-7 and HepG2 cell lines, comparing with the positive contrast
drugs, Celecoxib and Gefitinib. The IC50 of the compounds against
these four human cancer cells were summarized in Table 2. As
shown, the results revealed that most of the target compounds
exhibited significant anticancer activities, ranging from 1.90 to
50.61
anti-tumor activity in A549 cell lines with IC50 of 1.90
pared with the positive control Gefitinib (IC50 = 2.86 M) and Cele-
coxib (IC50 = 2.15 M). More potent anti-tumor activities for A549
together with virtual screening results indicated that the MMP-2/
lM. Especially, compound 3i behaved the most potent
l
M, com-
l
l
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X.-Q. Yan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
3
R1
R3
O
R1
H2N
HN
R2
SO2NH2
CH
HC
R3
R2
CHO
O
2a-2y
1a-1b
SO2NH2
N
N
R1
R3
R2
3a-3y
Scheme 1. Reagents and conditions: (a) 0.5 equiv 40% potassium hydroxide solution, ethanol, 1.0 equiv different substituted acetophenone, (b) acetic acid, ethanol, 1.2 equiv
4-sulfamoylphenyl hydrazine hydrochloride.
Figure 1. Crystal structure diagrams of compounds 3j, 3m and 3s.
Table 1
Crystal data for compounds 3j, 3m and 3s
Compounds
3j
3m
3s
Empirical formula
Formula weight
Temperature (K)
Crystal system
Space group
a (Å)
C
26H23N3O3S
C25H21N3O2S
427.52
273(2)
Monoclinic
P21/c (No.14)
5.5995(6)
21.282(2)
17.7413(17)
90.00
C25H20BrN3O2S
506.41
273(2)
Monoclinic
P21/c (No.14)
9.2897(6)
22.7295(14)
10.5959(6)
90.00
457.54
273(2)
Monoclinic
P21/c (No.14)
5.3526(4)
24.1464(16)
17.5540(16)
90.00
b (Å)
c (Å)
a
(°)
b (°)
(°)
93.964(2)
90.00
98.529(3)
90.00
92.995(2)
90.00
c
V (Å)
2263.4(3)
29
1.598
2090.9(4)
27
1.610
2234.3(2)
21
2.419
Z
Dcalcd/g cmꢀ3
h range (°)
F(000)
2.05–25.14
1102
2.24–25.27
1026
2.12–25.14
1533
Reflections collected
Data/restraints/parameters
Absorption coefficient (mmꢀ1
21015 (Rint = 0.0658)
4043/0/299
0.764
20029 (Rint = 0.1167)
3791/0/280
0.770
21235 (Rint = 0.0585)
3978/0/280
9.959
)
R1; wR2 [I >2
R1; wR2 (all data)
GOF
r
(I)]
0.0619/0.1495
0.1191/0.1769
1.026
0.0682/0.1343
0.1899/0.1753
1.007
0.1252/0.3951
0.1660/0.4237
1.679
Larg. peak/hole (e Å)
0.643/ꢀ0.388
0.318/ꢀ0.285
7.124/ꢀ0.697
MMP-9 might be potential targets which these sulfonamide
derivatives including dihydropyrazole moieties interacted with.
All the synthesized compounds (3a–3y) were tested for MMP-2/
MMP-9 inhibitions in comparison to the positive control group
CMT-1 under identical conditions. In this assay, the IC50 values of
the target compounds possessing potent inhibitory activity were
shown in Table 3. As shown, the results revealed that the majority
of the synthesized compounds exhibited significant inhibition
activities against MMP-2/MMP-9.
The following structure–activity relationship (SAR) could be
observed from data of Table 3, MMP-2/MMP-9 activities of these
compounds were tested against the standard clinically inhibitors
CMT-1. The physiologically dominant matrix metalloproteinases
were inhibited by compounds 3a–3y with IC50 ranging from 0.21
to 23.82
33.75 M for MMP-9.
Among these given compounds, compound 3i was the most
active with IC50 value of 0.21/1.87 M, which had stronger
lM for MMP-2, having with IC50 in the range of 1.87–
l
l
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X.-Q. Yan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
Table 2
Table 4
In vitro antiproliferation activities (IC50
,
l
Ma–c) of target compounds (3a–3y)
The median cytotoxic concentration (CC50) data of all compounds
a
a
Compounds R1
R2
R3
IC50
,
l
Ma–c
Compounds
CC50
(lM)
Compounds
CC50 (lM)
MCF-7 HeLa
A549
HepG2
3a
3b
3c
3d
3e
3f
3g
3h
3i
51.35
51.23
53.14
48.24
45.32
42.21
46.88
51.26
52.45
47.06
59.50
49.22
50.54
3n
3o
3p
3q
3r
3s
3t
3u
51.68
49.88
52.41
49.38
48.96
47.04
55.86
53.13
45.40
53.77
49.53
54.76
54.38
a
-Naphthyl
3a
3b
3c
3d
3e
3f
3g
3h
3i
H
H
H
H
H
H
H
H
H
H
CH3
OCH3
Br
I
H
H
H
22.62
20.16 12.91 19.08
CH3 10.03
6.37
29.07
9.87
2.84
7.38 10.03
3.14 5.83
5.82 36.42
8.19 14.92
6.83
7.77
1.9
6.51 27.76
3.33 8.66
5.38
Cl
H
H
H
H
H
23.61
8.63
26.14
28.83
18.06
9.89
30.6
28.75
26.04
8.61
3v
3w
3x
8.06
7.04
6.99
3j
3k
3l
CH3
CH3
OCH3
OCH2CH3
Cl
CH3 18.06
12.13
30.12
18.52
11.51
3y
3j
3k
3l
H
H
H
H
H
H
26.37
35.05
18.02
3m
Celecoxib
a
2.98 16.45
The cytotoxicity of each compound was expressed as the concentration of
compound that reduced cell viability to 50% (CC50).
b-Naphthyl
3m
3n
3o
3p
3q
3r
3s
3t
3u
3v
3w
3x
H
H
H
H
H
H
H
H
H
H
H
CH3
OCH3
F
Br
I
H
H
H
H
H
—
—
H
21.63
13.04
15.63
16.44
26.43
36.49
21.05
8.42 17.85
CH3 16.34
6.84
2.16 31.08
7.64 7.68
6.88
Cl
H
H
H
H
H
H
H
H
H
H
—
—
8.64
11.08
13.56
13.08
9.15
11.06
18.17
50.61
38.23
12.28
12.41
6.71
8.67 26.04
7.83 24.83
23.67 10.32 28.98
32.04 12.04 18.06
CH3
OCH3
OCH2CH3
F
Cl
—
—
17.56
6.90
9.31 22.32
35.35 17.82 9.17
8.32
35.35
26.11
19.21
1.52
6.95 20.66
2.76 25.03
3y
Gefitinib
Celecoxib
2.86
2.15
—
0.76
6.88
7.55
a
Antiproliferation activity was measured using the MTT assay. Values are the
average of six independent experiments run in triplicate. Variation was generally
5–10%.
b
Cancer cells kindly supplied by State Key Laboratory of Pharmaceutical
Biotechnology, Nanjing University.
c
Errors were in the range of 5–10% of the reported values, from six different
assays.
Table 3
Inhibition activities of compounds (3a–3y) against MMP-2/MMP-9
Compounds
IC50
,
l
Ma–c
MMP-9
Compounds
IC50
,
l
Ma–c
MMP-9
MMP-2
MMP-2
Figure 2. Compound 3i induced apoptosis in A549 cells with the density of 0, 2.0,
4.0, 16.0 lM. A549 cells were treated with for 24 h. Values represent the mean S.
D, n = 3, P <0.05 versus control. The percentage of cells in each part was indicated.
3a
3b
3c
3d
3e
3f
3g
3h
3i
7.92
2.91
8.63
3.24
4.83
11.36
9.43
6.81
0.21
4.27
0.81
2.70
12.63
10.89
5.43
11.97
4.29
6.72
7.97
12.87
15.96
1.87
8.61
3.19
3n
3o
3p
3q
3r
3s
3t
3u
3v
3w
3x
11.44
14.83
3.86
7.91
8.72
5.92
4.68
5.96
13.89
6.91
4.95
18.96
18.31
19.81
5.88
2.15
23.82
17.82
15.67
2.81
9.90
3j
3k
3l
14.94
16.84
3.60
5.47
33.75
3y
CMT-1
3m
1.26
2.52
a
MMP-2/MMP-9 inhibitory activity was measured using the Human Matrix
metalloproteinase 2 ELISA kit. Values are the average of six independent experi-
ments run in triplicate. Variation was generally 5-10%.
b
Errors were in the range of 5–10% of the reported values, from six different
assays.
c
Human recombinant enzymes, by the esterase assay (4-nitrophenylacetate as
substrate).
MMP-2/MMP-9 inhibition capability than the positive control drug
CMT-1 just with IC50 value of 1.26/2.52 lM. Based on the obtained
data, we simplified the situations by only treating the single sub-
stituent as the single factor to deal with. To begin with, sub-
stituents-R2, -R3 kept steady, the changes with different
Figure 3. The histogram about CDOCKER_INTERACTION_ENERGY (ꢀkcal/mol) of
compounds (3a–3y) for MMP-2.
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X.-Q. Yan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
5
substituents-R1 for antitumor activity showed the strong electron
donor on the para-position were better than electron acceptor or
weak electron donor on the same position. For instance, the active
assays. Furthermore, there is also a reasonable correlation coeffi-
cient between the two matrix metalloproteinases inhibitory activ-
ities. Thus, it is not amazing in view of the high sequence homology
of the catalytic domains of these two matrix metalloproteinases.
In comparison, we also found that these compounds with
gradients for compounds were 3k (IC50 = 0.81
(IC50 = 2.70 M) > 3a (IC50 = 7.92 M), 3w (IC50 = 14.94
(IC50 = 16.84
M). Furthermore, modifying merely substituents-R2
or -R3, the activity order was shown as follows: 3t (IC50 = 15.67
lM) > 3l
l
l
lM) > 3x
l
a-naphthyl generally exhibited more potent anticancer activities
than those having b-naphthyl. From the above-mentioned analysis,
the results of MMP-2/MMP-9 inhibitory activity of the tested com-
pounds correlated with the structure–activity relationships (SAR)
of their inhibitory effects on the cell proliferation assay. It could
l
l
M) > 3s (IC50 = 17.82
M) > 3h (IC50 = 6.81 M), 3b (IC50 = 2.91
M) > 3m (IC50 = 12.63 l
l
M) > 3r (IC50 = 23.82
M) > 3c (IC50 = 8.63
M). In view of electroneg-
l
M), 3i (IC50 = 0.21
l
l
lM),
3n (IC50 = 11.44
l
ativity of modified substituents, it was obviously observed that
the strong electron donor was very conducive to improve activity
correlated with MMP-2.
Besides, it was observed that the IC50 values for inhibition of
MMP-2 were higher than those observed of MMP-9 with the same
variation trend. It was evident that higher concentration of the
purified MMP-2 was used than that of MMP-9 in the enzyme
be concluded that the compounds with a-naphthyl were found
to be the more favorable for the anticancer activity.
All the target compounds (3a–3y) were evaluated for their tox-
icity against human kidney epithelial cell 293T with the median
cytotoxic concentration (CC50) data of tested compounds by the
MTT assay. As displayed in Table 4, these compounds were
tested at multiple doses to study the viability of macrophage and
Figure 4. The histogram about CDOCKER_INTERACTION_ENERGY (ꢀkcal/mol) of
compounds (3a–3y) for MMP-9.
Figure 6. Molecular docking 3D modeling of compound 3i with the MMP-2 binding
site: for clarity, only interacting residues are displayed.
Figure 5. Molecular docking 2D modeling of compound 3i with MMP-2: for clarity, only interacting residues are displayed.
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X.-Q. Yan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
Figure 7. Molecular docking 2D modeling of compound 3i with MMP-9: for clarity, only interacting residues are displayed.
Figure 8. Molecular docking 3D modeling of compound 3i with the MMP-9 binding site: for clarity, only interacting residues are displayed.
demonstrated almost no cytotoxic activities in vitro against human
kidney epithelial cell 293T.
0.3 Å. A 9.9 Å sphere of water molecules was added around the
ligand and a short (3 ps) dynamics run was carried out, followed
by several cycles of minimization of Quanta/CHARMM. The entire
protein–ligand complex was allowed to move during calculations.
The predicted binding interaction energy was used as the criterion
for ranking. The estimated interaction energies of other synthe-
sized compounds were ranging from ꢀ53.29 to ꢀ43.20, ꢀ48.37
to ꢀ39.56 kcal/mol, respectively, as displayed in Figures 3 and 4
with histogram. The selected compound of 3i had a best estimated
binding free energy of ꢀ53.29 kcal/mol for MMP-2 and
ꢀ48.37 kcal/mol for MMP-9. The binding mode of compound 3i
interacting with 1QIB protein was exhibited in Figures 5 and 6.
The amino acid residues which interacted with the MMP-2 were
labeled. In the binding mode, compound 3i was nicely bound to
the ATP binding site including one hydrogen bond with the back-
bone NH of Phe146 (angle O–Hꢁ ꢁ ꢁN = 148.52°, distance = 3.4 Å)
To confirm whether the inhibition of cell growth of A549 cell
lines was related to cell apoptosis, it was determined to adopt flow
cytometry of Annexin V-FITC/PI Apoptosis Detection Kit to induce
the A549 cell apoptosis with compound 3i. The uptake of Annexin
V-FITC/PI significantly increased, the uptake of normal cells was
significantly decreased in a time-dependent manner. According
to the data annotated, the percentage of apoptotic cells was mark-
edly elevated directly and markedly in a manner of dose-depen-
dent. As shown in Figure 2, the percentages of cell apoptosis
20.8%, 17.4%, 16.1%, 13.7% were responding to the concentration
of compound 3i 16.0, 4.0, 2.0, 0 lM, respectively.
To gain better understanding on the potency of the 25 com-
pounds, we examined the interaction of these compounds with
MMP-2/MMP-9 by molecular docking. It was performed on the
simulation between the compounds and the ATP binding sites in
MMP-2/MMP-9. The protein structures of the MMP-2/MMP-9 were
downloaded from the PDB (PDB code: 1QIB and 2OVX), and pre-
processed by the DS 3.5 (Discovery Studio 3.5, Accelrys, Co. Ltd.).
Hydrogens added to the structure, H-bonds within the protein
were optimized, and the protein was minimized to an RMSD of
and a
p-cation interaction between the backbone Phe157 (dis-
tance = 6.9 Å). Besides, one coordinate bond was formed between
zinc cation and oxygen atoms (distance = 2.5 Å), which increased
the binding affinity dramatically in theory, as displayed in Figure 6.
There was the binding mode of compound 3i interacting with
2OVX protein in Figures 7 and 8. As shown, three amino acids,
Please cite this article in press as: Yan, X.-Q.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.026

X.-Q. Yan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
7
Table 5
The Experimental and predicted inhibitory activity of compounds (3a–3y) by
3D-QSAR models based upon active conformation achieved by molecular docking
Compoundsa
MMP-2
Predicted pIC50
Residual error
Actual pIC50
3a
3b
3c
3d
5.10
5.54
5.07
5.49
5.32
5.09
5.54
5.04
5.54
5.08
0.01
0.00
0.03
ꢀ0.05
0.24
3e
3f
3g
4.95
5.03
5.17
4.88
5.00
5.28
0.07
0.03
ꢀ0.11
3h
3i
6.68
5.38
6.71
5.39
ꢀ0.03
ꢀ0.01
3j
3k
3l
6.10
5.57
4.90
5.83
5.50
5.08
0.27
0.07
ꢀ0.18
3m
3n
4.94
4.83
4.96
5.27
ꢀ0.02
ꢀ0.44
3o
3q
3p
3r
3s
3t
3u
3v
3w
3x
3y
5.68
5.42
4.62
4.75
4.81
5.55
5.00
4.83
4.77
5.44
5.67
5.46
4.65
4.72
4.91
5.54
4.97
4.81
4.87
5.38
0.01
ꢀ0.04
ꢀ0.03
0.03
Figure 9. Comparing the predicted pIC50 value about MMP-2 inhibitory activities
with that of the experiment by linear fitting curve.
ꢀ0.10
0.01
model possessed pretty good predicting capability. The relation-
ship between observed and predicted values had been shown
graphically in Figure 9.
0.03
0.02
ꢀ0.10
0.06
Also the molecules aligned with the iso-surfaces of the 3D-QSAR
model coefficients on electrostatic potential grids Figure 10(a) and
Van der Waals grids Figure 10(b) were listed. Electrostatic map
were depicted below to display the favorable (in blue) or unfavor-
able (in red) electrostatic field region in a contour plot, while the
energy grids corresponding to the favorable (in green) or unfavor-
able (in yellow) steric effects were also marked out. For com-
pounds based on the 3D-QSAR model, possessing strong Van der
Waals attraction in the green areas and a polar group in the blue
electrostatic potential areas mean achieving potent bioactivity.
This model was accordant with the actual situation for compounds.
Accordingly, this promising model would provide a guideline to
design and optimize more effective tubulin inhibitors and pave
the way for us in the further study.
In summary, novel series of sulfonamide derivatives including
dihydropyrazole moieties (3a–3y) had been evaluated for anti-
cancer activities against MCF-7, HeLa, A549, HepG2 cell lines
and MMP-2/MMP-9 inhibitory activities. These compounds
showed a very interesting profile for the inhibition of MMP-2/
MMP-9, which mostly exhibited potent anticancer and MMP-2/
MMP-9 inhibitory activities, with IC50 ranging from 1.90 to
a
The underlined for the test set, and the rest for training.
Leu397, Leu418 and His401, were of significance in the binding of
ligand with enzyme of 2OVX. Moreover, the Leu397 formed two
hydrogen bonds with 3i (angle Oꢁ ꢁ ꢁH–N = 132.7°, distance = 2.5 Å,
angle Oꢁ ꢁ ꢁH–N = 92.5°, distance = 4.2 Å). Furthermore, compound
3i was also bonded with Leu418 by a hydrogen (angle Oꢁ ꢁ ꢁH–
N = 112.4°, distance = 2.2 Å) and His401 by a Pi bond. As exhibited
in Figure 8, there was also a ATP binding site of a coordinate bond
between zinc cation and nitrogen atoms (distance = 2.3 Å). Accord-
ing to the above, these molecular docking results along with the
biological assay data suggested that compound 3i might be a
potential inhibitor of the MMP-2.
In order to obtain the systematic SAR profile on sulfonamide
derivatives containing dihydropyrazole moieties (3a–3y) as antitu-
mor agents and explore the more powerful and selective inhibitors
of MMP-2, 3D-QASR models37 were built according to the com-
pounds synthesized and their corresponding capability. By this
effort, we intended to explain the mechanism of the SAR and cast
a light on the discovery of more potent novel antagonist of
MMP-2. This model was performed by built-in QSAR software of
DS 3.5 with all the molecular converted to the active conformation
50.61 lM, 0.21 to 23.82 lM and 1.87 to 33.75 lM, respectively.
Moremore, most of them showed almost no toxicity towards
293T. Among them, compound 3i exhibited the most potent
MMP-2/MMP-9 inhibition activities (IC50,MMP-2 = 0.21
lM, IC50,
and corresponding pIC50
(lM) values, which were converted from
MMP-9 = 1.87 M). Besides, the probable binding models and poses
l
the obtained IC50 M) values of MMP-2 inhibition. These com-
(l
were obtained by docking simulation. Analysing the binding
model of compounds 3i with MMP-2, there were a hydrogen
bond, a p-cation interaction with the protein residues and a coor-
pounds were divided into a test set composing 20 agents and a rel-
ative training set including 5 agents by the random, which had
been presented in Table 5.
dinate bonds with Zinc Ion in the ATP binding site, which might
play a crucial role in its MMP-2 inhibition and antiproliferative
activities. Furthermore, three hydrogen bonds, a Pi bond and a
coordinate bonds with Zinc Ion formed the major acting force in
the binding model of compounds 3i with MMP-9. Last but not
least, 3D-QASR models were built with previous activity data
and binding conformations to begin our work in this paper as well
as to provide a reliable tool for reasonable design and synthesis of
potent MMP-2 inhibitors.
By default, the alignment conformation of each molecule pos-
sessed the lowest CDOCKER_INTERACTION_ENENGY among all of
the docked poses. The critical regions (steric or electrostatic)
affecting the binding affinity was gained by this 3D-QSAR model.
Exerting CHARMM force filed and PLS regression, the model was
set up with the correlation coefficient R2 is 0.922, and the leave-
one-out cross validation coefficient q2 is 0.469. Besides, the RMS
error, the mean absolute error, R2
and F are 0.249, 0.214,
pred
0.834 and 101.916, respectively. These details indicated that this
Please cite this article in press as: Yan, X.-Q.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.026

8
X.-Q. Yan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
Figure 10. (a) Isosurface of the 3D-QSAR model coefficients on electrostatic potential grids. Blue represents positive coefficients; red represents negative coefficients. (b)
Isosurface of the 3D-QSAR model coefficients on Van der Waals grids. Green represents positive coefficients; yellow represents negative coefficients
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Please cite this article in press as: Yan, X.-Q.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.026