A water-soluble metal–organic coordination polymer of Zn(II) Schiff base complex in interaction with DNA: diagnosing the mode of binding by in vitro studies

Article abstract of DOI:10.1007/s13738-019-01716-0

In this paper, in vitro DNA binding of a water-soluble metal–organic coordination polymer of Zn(II) Schiff base complex was considered. By focusing on the cooperative effect of multi-Zn(II) centers of the complex, the affinity and mode of binding were investigated by some techniques, e.g., absorption and fluorescence spectroscopy, circular dichroism spectroscopy, viscosity measurement, molecular docking, iodide quenching studies and effect of ionic strength on the complex–DNA binding. The calculated value of K_b = 1.3 × 10³?M^?1 represented a good affinity of the Zn(II) complex to DNA. From the experimental methods and docking studies, non-classical intercalation (i.e., van der Waals interactions, groove binding or external binding) was proposed as the main mode of binding.

Full text of DOI:10.1007/s13738-019-01716-0

Journal of the Iranian Chemical Society
https://doi.org/10.1007/s13738-019-01716-0
ORIGINAL PAPER
A water‑soluble metal–organic coordination polymer of Zn(II)
Schif base complex in interaction with DNA: diagnosing the mode
of binding by in vitro studies
Zahra Asadi1 · Neda Nasrollahi1 · Maryam Golchin1
Received: 22 September 2018 / Accepted: 17 June 2019
© Iranian Chemical Society 2019
Abstract
In this paper, in vitro DNA binding of a water-soluble metal–organic coordination polymer of Zn(II) Schif base complex
was considered. By focusing on the cooperative efect of multi-Zn(II) centers of the complex, the afnity and mode of bind-
ing were investigated by some techniques, e.g., absorption and fuorescence spectroscopy, circular dichroism spectroscopy,
viscosity measurement, molecular docking, iodide quenching studies and efect of ionic strength on the complex–DNA
binding. The calculated value of Kb =1.3×103 M−1 represented a good afnity of the Zn(II) complex to DNA. From the
experimental methods and docking studies, non-classical intercalation (i.e., van der Waals interactions, groove binding or
external binding) was proposed as the main mode of binding.
Keywords Metal–organic coordination polymer · Zn(II) · Schif base · DNA binding · Docking · Fluorescence spectra
Introduction
polymers (NCPs) as nanomaterials in the nano-medicine
feld has been reported recently. The unique characteristics
of these nanomaterials are intrinsic biodegradability, chem-
ical diversities and specially porous structures, which are
very important in drug delivery process [8]. Besides them,
a class of efective carriers of drug is metal–organic frame-
works (MOFs) and their special characteristics such as the
porosities, large surface areas and harmonic functionalities
make them fantastic carriers [9–14].
Metal–organic coordination polymers (MOCPs) consist of
metal ions connected by coordinated ligands to an unlimited
order. Generally, the formation of MOCP proceeds automati-
cally through a self-assemble process. The MOCPs have a
variety of architectures from simple one-dimensional chains
which are usually created with small ligands to mesoporous
frameworks like metal–organic frameworks (MOFs) [1].
Therapeutic applications of metal complexes attract much
interest since the discovery of anticancer activity of cispl-
atin. Research on the anticancer agents reveals that metal
complexes are more efective than free metal compounds
[2–4], and also multinuclear complexes reveal increasing
efciency and selectivity in metallo-nuclease ability and
anticancer activity, because of the cooperation between
metal centers [5–7]. The use of nano-scaled coordination
Undesired side efects of mononuclear platinum-based
drugs such as cisplatin, oxaliplatin and carboplatin have
limited their clinical use. Thus, trying to develop other plati-
num anticancer drugs (mononuclear and/or multinuclear)
with less toxicity, less cross resistance and efcient activity
has been increased [15–17]. A new research on multinuclear
platinum complexes bridged by aliphatic diamines reveals
higher cytotoxic activity against diferent cell lines [18].
This cooperation between two or further metal centers
enhances the enzymatic activity of hydrolytic enzymes such
as polymerases, topoisomerases and recombinases [19–21].
Also it is shown that some hydrolytic enzymes have the
ability to cleavage the phosphate ester bonds. In the active
sites of such enzymes, two or more transition metal ions are
located which cooperatively operate as Lewis acid sites in
the catalytic process [22–26].
Electronic supplementary material The online version of this
article (https://doi.org/10.1007/s13738-019-01716-0) contains
supplementary material, which is available to authorized users.
* Zahra Asadi
zasadi@shirazu.ac.ir
1
Department of Chemistry, College of Sciences, Shiraz
University, Shiraz 71454, Iran
Vol.:(0123456789)
1 3

Journal of the Iranian Chemical Society
One important aspect in mimicking the enzymatic process
is the extent of collaboration between the metal centers, and
thus, it is reasonable that di- and tri-nuclear complexes are
more active than their mononuclear counterparts [27–29].
Di- and tri-centered zinc(II) complexes are more impor-
tant than other 3d transition metal complexes, and this
importance is regarded to the fact that zinc and iron are the
most abundant transition metals in living cells. The strong
Lewis acidity of zinc(II), some strange chemical properties,
such as rapid exchanging of ligands in Zn(II) complexes,
diferent manners of coordination, the absence of redox
behavior under physiological conditions and the existence
of zinc(II) in all enzyme classes attract more attention to its
complexes especially in biological studies [30–36].
Interaction of metal complexes with DNA is the topic of
many biological projects as the results of such studies could be
potentially used in metal-based drug design. Continuing our
studies in this feld, the interaction of a water-soluble Zn(II)
coordination polymer with DNA was investigated herein.
Experimental section
General methods and materials
The coordination polymer was prepared by the condensation
of 2,6-diformyl-4-methylphenol, glycine and zinc(II)chloride
as previously reported. The CCDC number and all crystal-
lographic data were reported there [41]. All used materials
and instruments were mentioned in supporting information.
The synthetic route to the compounds is shown in Scheme 1.
One of the strategies in designing the multinuclear
complexes is the use of multi-dentate Schif base ligands
which can easily arrange around the metal centers and
make unusual confgurations [37]. The Schif base ligands
are treated as the most signifcant ligands as they possess
diferent coordinating atoms. Thus, the Schif base ligands
and their metal complexes have notable importance in the
evaluation of the coordination chemistry [38]. Metal Schif
base complexes are of great importance in the coordination
chemistry because of their stability, structural variability,
ease of preparation and a variety of applications [39] like
biological activities including antifungal, antibacterial, anti-
malarial, antiproliferative, anti-infammatory, antiviral and
antipyretic properties. Many Schif base complexes show
excellent catalytic activity in various reactions and in the
presence of moisture [40].
Synthesis of 2,6‑diformyl‑4‑methylphenol
P-cresol (10.8 g, 0.1 mol) was dissolved in acetic acid
(50 cm3), and then hexamethylenetetramine (28.2 g, 0.2 mol)
and paraformaldehyde (30 g, 1.0 mol) were added succes-
sively. After producing a light-brown viscous solution, heat-
ing (70–90 °C) was continued for 2 h and then conc. H2SO4
(10 cm3) was added to the cooled solution. An additional
0.5 h refux was performed and then treated with distilled
water (400 cm3) to a light-yellow precipitate, which was
stored at 4 °C overnight. The yellow product was isolated by
fltration and washed with a small amount of cold methanol.
Scheme 1 Synthetic route to
CH3
CH3
the compounds
H
N
N
+
OH
C
H
O
H
N
N
+
n
O
OH
O
OH
CH3
CH3
N
O
N
Zn
Zn
O
ZnCl2
reflux
O
O
O
O
O
O
O
O
O
O
N
+
H2N
OH
Zn
Zn
O
N
O
OH
O
CH3
1 3

Journal of the Iranian Chemical Society
A purer product was obtained after recrystallization from
toluene.
increased (from 2.15 to 12.65 μM). An Ostwald viscom-
eter was used for viscosity measurement and immersed
in a thermostated water bath maintained to 25.0 0.1 °C.
The DNA concentration was fxed at 10 μM, and fow time
was measured with a digital stopwatch. The measurements
were carried out three times for each sample to calculate
the average fow time.
Yield: 5.7 g (35%); color: yellow; m.p: 130–134 °C (lit.,
133.5 °C) [42]; 1H NMR [250 MHz, DMSO-d6, δ (ppm)]:
11.38 (s, 1H, OH), 10.19 (s, 2H, HC=O), 7.82 (s, 2H,
1
Ar–H), 2.31 (s, 3H, CH3); HNMR (CDCl3, ppm): 11.39
(s, 1H, OH), 10.15 (s, 2H, HC = O), 7.70 (s, 2H, Ar–H),
2.32 (s, 3H, CH3); FT-IR (KBr, cm−1): 2869 (υC–H), 1674
(υC=O), 1211 (υC–O); Elemental Analysis, found (Calc.) %:
C9H8O3 (MW=164.05 g mol−1) C: 66.02 (65.85); H: 4.78
(4.91); N: 0 (0).
Molecular docking calculation was performed using the
Molegro Virtual Docker (MVD) software [43]. From the
Protein Data Bank (www.rsbs.org/pdb), the crystal struc-
ture of DNA with PDB code: 4HC9 d(TTTTTGGCCCCC
AAAAAAAA) was downloaded [44] and water and pro-
tein molecules at this strand were removed before perform-
ing docking calculations [45]. Bonding site was chosen
at (x = 8, y = − 107, z = 50 and radius = 28). The score as
Moldock score with GRID resolution of 0.3 Å was chosen,
and the number of runs for each docking calculation was
equal to 20 and ten diferent poses were requested. All
other parameters were kept at their default values.
Synthesis of coordination polymer
2,6-diformyl-4-methylphenol (0.16 g, 1 mmol) in 20 mL
ethanol and glycine (0.15 g, 2 mmol) in 10 mL water was
refuxed for 3 h, and then zinc(II) chloride (0.27 g, 2 mmol)
was added. A yellow solid precipitate was collected by fltra-
tion after solvent evaporation and washed with cold ethanol
and diethyl ether. Yellow crystals suitable for X-ray crystal-
lography were obtained by recrystallization in water.
Yield: 0.53 g (48%); color: yellow; m.p: 280 °C; FT-IR
(KBr, cm−1): 3448 (υOH), 1658 (υC=O), 1542 (υC=N); Ele-
mental Analysis, found (Calc.) %: C26H24N4O10Zn2.4H2O
(MW = 755.33 g mol−1) C: 41.85 (41.34); H: 4.36 (4.27);
N: 7.59 (7.42).
The cytotoxicity assay
The growth inhibitory efects of the complex against three
cell lines including Jurkat human T cell leukemia, Raji
Burkitt’s lymphoma and A549 lung carcinoma were exam-
ined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetra-
zolium bromide (MTT) assay as previously described
[46]. The cell lines were cultured in RPMI 1640 medium
(Sigma, St. Louis, MO) supplemented with 10% fetal calf
serum (Gibco, Berlin, Germany). Cells were maintained
at 37 °C with 5% CO2 and 95% humidity. The cells were
fed until confuent and expanded by trypsinization (for
A549) and then subcultured at lower numbers in new cul-
ture fasks. A predetermined number of cells (15 × 103 for
Jurkat and Raji cells and 7.5 × 103 for A549 cells) were
seeded in the wells of a 96-well plate with varying concen-
trations of the complex (0.1–100 µg/mL) and incubated at
37 °C with 5% CO2 for 48 h. Cells treated only with dime-
thyl sulfoxide (solvent) at a concentration equal to the test
wells were used as negative control and those treated only
with cisplatin as positive control. Ten microliters of MTT
solutions (5 mg mL−1 in RPMI medium) was added to each
well, and incubation was continued for 4 h. At the end,
the produced insoluble formazan was dissolved by adding
DMSO and shaking for 10 min. Then, the optical density
(OD) was read at 570 nm with a reference wavelength of
630 nm in a microplate reader (Bio-Tek’s ELx808, VT).
To calculate the percentage of growth inhibition, the equa-
tion: [1 − (test OD/negative control OD)] × 100 was used.
From the graph of inhibition percentage against diferent
compounds concentrations, the 50% cell inhibition (IC50)
value was calculated.
DNA‑binding experiments
The absorption (UV–Vis) spectroscopy was performed at
fxed temperature of 25 °C. The stock solution of complex
(1.0 × 103 μM) was prepared by dissolving an appropriate
amount of the complex in 10 mL DMSO/Tris-HCl bufer
(50:50 v/v) solution. For UV–Vis spectroscopy, the stock
solution was diluted to 40 μM with Tris-HCl bufer. Vari-
ous concentrations of HS-DNA ranging from 0 to 1000 µM
were added to the complex solution for UV–Vis titration.
The concentration of HS-DNA was calculated by using
its extinction coefcient at 260 nm (6600 M−1cm−1). The
solution of HS-DNA in Tris-HCl bufer gave a ratio of
UV absorbance at 260 and 280 nm (A260/A280) equal to
1.9 that indicated the DNA was sufciently free from pro-
tein. All other experiments were done at room temperature
at constant concentration of complex solution at 0.4 μM
at Tris-HCl bufer. Fluorescence quenching spectra were
monitored in the range of 420 to 640 nm by focusing on
the changes in fuorescence intensity at 527 nm (excited
at 431 nm). The ionic strength studies were performed by
monitoring the changes in fuorescence intensity of a mix-
ture of complex (0.4 μM) and DNA (200 μM) by increas-
ing the concentration of NaCl from 4.7 to 18.8 μM. This
binary solution was also used for studying the quench-
ing efect of iodide ion (I−) when the concentration of KI
1 3

Journal of the Iranian Chemical Society
b = 1 + Kb Ct + Kb[DNA] / 2s
Results and discussion
(1b)
In this equation, the absorption coefcient is denoted by
εa, εb and εf for the absorption band (at a given DNA concen-
tration) for the complex in its free form and for the complex
in the fully bound form, respectively. The total concentration
of the metal complex nominates Ct, and s is the binding site
size. A plot of (εa −εf)/(εb −εf) versus [DNA] is shown in
Fig. 2.
Absorption spectroscopic studies
In many DNA interaction studies, UV–Vis absorption
spectroscopy has been employed as a simple instrumental
technique which is used for either studying the DNA stabil-
ity or drug–DNA interactions. In this method, the changes
in UV–Vis absorption spectra of the drug or DNA have
been monitored. An easy way to investigate the interac-
tion between drug and DNA is comparing the shift in the
maximum of the absorption band of drug when it is free
in solution or is bound to DNA [47]. The extent of this
shifting could be related to the strength of the interaction
between DNA and drug. Figure 1 describes the interaction of
Zn(II) complex with DNA. The absorption band at 434 nm
revealed a redshift (bathochromism) of about 4 nm along
with hypochromism. Also an isosbestic point at 380 nm was
observed. These spectral changes proposed covalent binding
of complex to DNA or intercalation in which a strong stack-
ing interaction between the aromatic chromophore of the
complex and base pairs of DNA occurred [48]. At 350 nm,
a hyperchromic efect of the band with a slight blueshift was
observed. Hyperchromism along with hypsochromism pro-
posed an electrostatic attraction or groove binding between
Zn(II) complex and DNA which can cause changes in DNA
conformation including partial uncoiling of the helix struc-
ture of DNA [49, 50]. Therefore hypochromic and hyper-
chromic efects with red shift and blue shift, respectively,
and the existence of an isosbestic point leading to a strong
interaction.
The intrinsic binding constant was calculated as
Kb = 1.3 × 103 M−1, and s value is 1.5. The Kb value for
ethidium bromide as a classical intercalator is 7×107 M−1
which is much larger than the Kb of Zn(II) complex. But
the Kb value for the Zn(II) complex is comparable to
some transition metal complexes either mono- or mul-
ticenters like: [Zn(Pyimpy)2](ClO4)2.C6H5CH3.0.5H2O,
Kb = 2.86 × 103 M−1 with the covalent mode of bind-
ing [53], [Cu(H2L1)Cl].CH3OH Kb = 2.28 × 103 M−1
,
[Cu4(HL2)2(H2L2)2(H2O)(C2H5OH)].2ClO4.2(C2H5OH)
Kb = 1.35 × 104 M−1, [Ni2(H2L1)2(OAc)2(C2H5OH)2]2
Kb = 2.39 × 103 M−1, [Ni4(HL2)3(μ3-O)(H2O)3].9H2O,
Kb = 2.55 × 103 M−1, with the intercalation mode of bind-
ing [54], [CuL1](ClO4) Kb = 8.4 × 103 M−1, [CuL4](ClO4)
Kb =1.9×104 M−1, [CuL5](ClO4) Kb =3.0×104 M−1, all of
which act as metallointercalators [55].
Fluorescence spectral studies
Fluorescence spectroscopy is most commonly used to study
the interaction of the complexes and biomolecules like DNA.
Higher sensitivity and selectivity of this technique in com-
parison with other techniques are its superiority. The com-
pounds containing aromatic functional groups reveal useful
fuorescence spectra. The mode of binding of the complexes to
DNA can be studied by fuorescence spectroscopy, and some
analytical tools base of emission spectra, e.g., fuorescence
resonance energy transfer (FRET), can recommend the ori-
entation of complex or its closeness to the DNA base pairs.
Besides the qualitative investigation of the interaction, by
calculating Kb, an insight into quantitative investigation was
prepared by using Eq. (1a, 1b) [51, 52]:
(
)
ꢀ
(
) (
)
(
)
ꢀa − ꢀf ∕ ꢀb − ꢀf
=
b −
b2 − 2Kb2Ct[DNA]∕s ∕2Kb Ct
(1a)
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
1.20E+00
8.00E-01
4.00E-01
0.00E+00
Free complex
0
0
0.0004
0.0008
0.0012
280
330
380
wavelength(nm)
430
480
[DNA]/M
Fig. 2 Plot of (εa −εf)/(εb −εf) versus [DNA] for the titration of the
Fig. 1 UV–Vis titration of Zn(II) complex with HS-DNA (0 to
1000 μM) in Tris-HCl bufer at 25 °C
complex with HS-DNA
1 3

Journal of the Iranian Chemical Society
The emission spectra of the complexes are very sensitive to
the surrounding environment. The signifcant spectral shift
(10–15 nm) is caused by transfer of the complex in the medium
with large diferent polarities. From Fig. 3, about 14 nm shift
was observed for emission spectra of the complex (4×10−7 M)
(at 527 nm) upon addition of DNA which confrms the difer-
ence in the polarity of the complex environment. By increas-
ing the concentration of HS-DNA to the complex solution,
emission band at 450 nm was slightly enhanced and at about
527 nm obviously quenched (Fig. 3). Quenching of the fuo-
rescent spectra is due to groove binding, hydrogen binding,
electrostatic interactions or hydrophobic interactions. All these
modes of binding implied that the complex was located in
close proximity to the sugar phosphate backbone of DNA. The
small enhancement of the fuorescence intensity at 450 nm
revealed the possibility of the intercalation of the complex (or
part of the complex) between base pairs of the helix.
3.5
3
2.5
2
1.5
1
0.5
0
0.0002 0.0004 0.0006 0.0008 0.001
[DNA]
Fig. 4 Stern–Volmer plot of the complex, by employing the emission
data at 527 nm at room temperature
1∕(F0 − F) = 1∕F0Kb [Q] + 1∕F0
(3)
Solvent water molecules potentially can quench the emis-
sion spectra of the complex but because of the penetration of
the complex into the hydrophobic environment inside the HS-
DNA, this efect is inhibited. Stern–Volmer Eq. (2) was used
to analyze the emission data:
where F0 and F are the fuorescence intensities in the absence
and presence of the quencher, [Q] is the concentration of
the quencher and Kb is the binding constant calculated from
the ratio of the intercept to the slope (Kb = 2.2 × 103 M−1)
(Fig. 5).
F0
= 1 + KSV [Q] = 1 + Kqꢀ0[Q]
(2)
F
Iodide quenching studies
where F and F0 are the fuorescence intensities in the pres-
ence and the absence of the quencher, respectively. KSV is the
Stern–Volmer quenching constant, [Q] is the concentration
of quencher, Kq is the bimolecular quenching constant and
τ0 is the average lifetime of biomolecule in the absence of
the quencher, and its value is 10−8s [56, 57]. The nonlinear
Stern–Volmer plot (Fig. 4) confrmed the existence of two
modes of interaction, static and dynamic, between the com-
plex and HS-DNA [58] which enabled the calculation of the
Stern–Volmer constant (KSV) and quenching rate constant
(Kq) [59, 60].
To further investigate the mode of binding, the interaction
of well-established quenchers like halide ions with the mix-
ture solution of complex–DNA was studied. The base of
this method is that the out site binders are more accessible
to the quencher, but groove binders and especially intercala-
tors are less accessible to the quenchers. The accessibility
refers to the fact that the intercalators are located between
base pairs of DNA and are protected from quenchers [61,
62]. From Fig. 6, it is obvious that the emission intensity
of complex–DNA solution in the absence and presence of
Thus, Lineweaver–Burk (LWB) Eq. (3) was used [60]:
0.016
Free complex
y = 1E-06x + 0.0022
400
0.012
0.008
0.004
0
R² = 0.9828
300
200
100
0
420
470
520
570
620
0.00E+00 2.00E+03 4.00E+03 6.00E+03
Wavelength/nm
[Q]
Fig. 3 Fluorescence titration spectra of the complex (4×10−7 M)
at 527 nm and 450 nm (excited at 431 nm) with HS-DNA (0 to
1000 μM) in Tris-HCl bufer at room temperature
Fig. 5 Lineweaver–Burk (LWB) plot at λ=527 nm for the complex at
room temperature
1 3

Journal of the Iranian Chemical Society
emission peak was observed. Thus, an electrostatic interac-
tion was concluded.
465.37
465
463.67
463.37
462.24
462
461.7
Circular dichroism (CD) spectra
It is obvious that during drug–DNA interactions, the mor-
phology of DNA changes to some extent. A useful technique
for diagnosing these changes and proposing the mode of
binding is circular dichroism (CD). It means that drug–DNA
interactions can afect the structure of DNA and thus the
intrinsic CD spectrum of DNA must be changed. The intrin-
sic CD spectrum of HS-DNA is characterized by a positive
band at 275 nm assigned to the base stacking and a nega-
tive band at 245 nm assigned to the right-handed helicity
of B-form DNA, in which the latter is very sensitive to the
mode of drug–DNA binding [63]. Electrostatic interaction
or groove binding of complexes with DNA reveals less or
no alteration on the helicity band or base stacking band but
intercalators perturb both the bands [63]. As revealed in
Fig. 8, by addition of the Zn(II) complex to the DNA solu-
tion, no signifcant changes in the form and no distinguished
shift in the CD spectrum of B-DNA were recognized, which
indicated that the HS-DNA kept the double-helix B-form
structure in the presence of Zn(II) complex. Thus, the pos-
sible mode of binding was concluded as groove binding or
electrostatic interaction.
Fig. 6 Fluorescence intensity plots of iodide quenching efect at room
temperature. Complex (0.4 μM)-DNA(200 μM) and increasing the
concentration of KI (2.15 to 12.65 μM)
increasing concentrations of potassium iodide decreases
mildly which confrmed the groove binding.
Efect of ionic strength on the complex–DNA binding
DNA is actually an anionic polyelectrolyte because of its
phosphate backbone; thus, if a molecule binds to DNA
through electrostatic attraction, then the change in ionic
strength of the medium can afect the mode of binding. In
human body, NaCl controls the ionic strength of the serum.
An electrostatic interaction exists between cationic spe-
cies (Na+) and the negatively charged phosphate backbone
of DNA which can compete with the electrostatic binding
between complex and DNA. Thus, by monitoring the spec-
tral changes of the mixture of complex and DNA solution
upon increasing the NaCl concentration, this competition
can be evaluated. Figure 7 reveals that with increasing
the NaCl concentration, an increase in the intensity of the
Molecular docking
One important step in drug-designing studies is molecular
docking investigations. In this scafold, locating a small
molecule (complex) in the potential binding sites of a target
molecule, e.g., DNA, is studied theoretically mainly in a
non-covalent mode of binding. Binding a small molecule
to the minor groove of DNA is an important tool to rec-
ognize DNA sequence [64]. Molecular modeling allows
600
500
DNA
14
9
DNA+20µM complex
DNA+40µM complex
Complex-DNA
400
300
200
100
0
4
-1
-6
400
450
500
550
600
650
Wavelegth/nm
230
250
270
290
310
330
wavelength(nm)
Fig. 7 Efect of change in ionic strength of the medium by increasing
the NaCl concentrations (4.7 to 18.8 μM) on the emission spectra of
the mixture of complex (0.4 μM) and DNA (200 μM) at room tem-
perature
Fig. 8 Efect of Zn(II) complex on CD spectra of HS-DNA (200 μM)
with varying concentrations of the complex at room temperature
1 3

Journal of the Iranian Chemical Society
the ligand fexibility and implies calculating the minimum
energy of the ligand in the active site of DNA. In this study,
the structure of the Zn(II) complex was obtained from its
X-ray crystallography fle (cif fle) and the binding mode
was predicted with DNA duplex with sequence d(TTTTTG
GCCCCCAAAAAAAA). The molecular docking studies
of the Zn(II) complex with DNA were performed, and the
energetically favorable docked pose of the complex is shown
in Fig. 9. The energy-minimizing docked pose revealed that
the complex was located in the minor grooves of DNA. It is
worthy to note that electrostatic attraction between positive
charge of Zn(II) atoms and the negative oxygen atoms of
the phosphate backbone of DNA makes favorable the bind-
ing of the complex. Also, Schif base ligands containing N
and O atoms caused van der Waals interactions and hydro-
phobic contacts with DNA functional groups. The more
favorable relative binding energy for the docked complex
was −81.22 kcal/mol, and the binding energy for all poses of
the docking (Table S1) was negative (values from −56.65 to
−81.22 kcal/mol for ten poses) that indicated a high binding
potential for Zn(II) complex to HS-DNA.
viscosity [65, 66]. The values of relative specifc viscosity
(η/η0)1/3, here η is viscosity of pure DNA and η0 is the vis-
cosity of DNA in the presence of the diferent concentrations
of complex, were plotted against r (r=[complex]/[DNA]).
From Fig. 10, it is concluded that non-classical intercalation
(i.e., van der Waals interactions, groove binding or external
binding) was the main mode of binding [67].
Inhibitory efects of the complex on various cancer
cell lines
The anticancer properties of complex have been already
proved [68–72]. In the current study, the synthetic complex
was also screened for its anticancer activities on A549,
Jurkat and Raji cell lines as the target. The cell lines were
incubated in the presence of increasing concentrations of
the complex for 48 h, and then cytotoxicity was measured.
1.02
1.015
1.01
1.005
1
Viscosity measurement
A critical test in proposing the mode of binding of the
small molecules to DNA is viscosity measurement which
is a hydrodynamic measurement that is very sensitive to
the DNA length change. Classical intercalators are located
between DNA base pairs and cause an increase in the length
of DNA and concomitantly its viscosity. But non-classical
intercalators cause bending (or kinking) of the DNA helix
and reduce the length of DNA and concomitantly its viscos-
ity. Groove binders located in the grooves of DNA cause
less changes (positive or negative) or no changes in DNA
0.995
0
0.05
0.1
0.15
0.2
0.25
r
Fig. 10 Efects of increasing amounts of complex (0–2.34 μM) on the
viscosity of DNA (10 μM) in 1 mM Tris-HCl bufer. (r=0.0–0.23) at
25 ℃
Fig. 9 Computational dock-
ing models (using the UCSF
Chimera software) illustrating
the mode of interaction between
DNA and Zn(II) complex
1 3

Journal of the Iranian Chemical Society
In Figs. 11, 12 and 13, the inhibitory efects of the com-
plex against cancer cell lines are shown. Generally, the
complex showed strong growth inhibitory activity against
the cell lines. In order to compare the cytotoxic efects of
the complex, the IC50 values were determined. IC50 value
is defned as the concentration of a compound where 50%
of the cell growth is inhibited. The complex had a stronger
activity against leukemia lymphoma cells (IC50, 7.3 μg/
mL for Jurkat and 9.3 μg/mL for Raji) compared to A549
(IC50, 93.6 μg/mL) based on the IC50 values. The IC50
values of cisplatin for A549 cell line were 79.4 μg/mL,
25 μg/mL for Jurkat and 30 μg/mL for Raji cells.
A549
Conclusion
100.00
In this study, interaction of a water-soluble metal–organic
coordination polymer of Zn(II) Schif base complex with
HS-DNA was assessed using absorption, emission and CD
spectroscopy, viscosity measurement and molecular docking.
To further investigate the mode of binding, iodide quenching
studies and the efect of ionic strength were done. By using
the UV–Vis spectral data, Kb =1.3×103 M−1 was calculated
as a confrmation of complex–DNA binding. From all the
used methods, non-classical intercalation is confrmed as
the main mode of binding. This result was further confrmed
by docking studies with suggested binding mode of groove
binding and binding energy of −81.22 kcal/mol. Our results
are useful in drug design with the main point of view that
the multinuclear complexes can be considered as potential
candidate for metal-based drugs.
80.00
60.00
40.00
20.00
0.00
0.1
1
10
25
50
100
-20.00
Concentation(µg/ml)
Fig. 11 Growth inhibitory activity of complex against A549 cancer
cell line
Jurkat
100.00
Acknowledgements We are grateful to the Shiraz University Research
Council for its fnancial support.
80.00
60.00
40.00
20.00
0.00
References
1. M.Y. Masoomi, A. Morsali, Coord. Chem. Rev. 256, 2921 (2012)
2. Z. Mandegani, Z. Asadi, M. Asadi, H.R. Karbalaei-Heidari, B.
Rastegari, Dalton Trans. 45, 6592 (2016)
0.1
1
10
25
50
100
-20.00
Concentration(µg/ml)
3. Z. Asadi, N. Nasrollahi, J. Mol. Struct. 1147, 582 (2017)
4. N. Shahabadi, S. Kashanian, F. Darabi, Eur. J. Med. Chem. 45,
4239 (2010)
Fig. 12 Growth inhibitory activity of complex against Jurkat cancer
5. A. Arbuse, M. Font, M.A. Martínez, X. Fontrodona, M.J. Prieto,
V. Moreno, X. Sala, A. Llobet, Inorg. Chem. 48, 11098 (2009)
6. K. Suntharalingam, A.J. White, R. Vilar, Inorg. Chem. 49, 8371
(2010)
cell line
7. A.K. Gorle, A.J. Ammit, L. Wallace, F.R. Keene, J.G. Collins,
New J. Chem. 38, 4049 (2014)
Ragi
100.00
8. J. Zhao, Y. Yang, X. Han, C. Liang, J. Liu, X. Song, Z. Ge, Z. Liu,
A.C.S. Appl, Mater. Interfaces 9, 23555 (2017)
9. X. Chen, R. Tong, Z. Shi, B. Yang, H. Liu, S. Ding, X. Wang,
Q. Lei, J. Wu, W. Fang, A.C.S. Appl, Mater. Interfaces 10, 2328
(2018)
80.00
60.00
40.00
20.00
0.00
10. S. Rojas, I. Colinet, D. Cunham, T. Hidalgo, F. Salles, C. Serre,
N. Guillou, P. Horcajada, ACS Omega 3, 2994 (2018)
11. Y. Yang, Q. Hu, Q. Zhang, K. Jiang, W. Lin, Y. Yang, Y. Cui, G.
Qian, Mol. Pharm. 13, 2782 (2016)
12. S. Rojas, F.J. Carmona, C.R. Maldonado, P. Horcajada, T.
Hidalgo, C. Serre, J.A. Navarro, E. Barea, Inorg. Chem. 55, 2650
(2016)
0.1
1
10
25
50
100
Concentration(µg/ml)
13. C. Adhikari, A. Das, A. Chakraborty, Mol. Pharm. 12, 3158
(2015)
Fig. 13 Growth inhibitory activity of complex against Ragi cancer
cell line
1 3

Journal of the Iranian Chemical Society
14. D.J. Levine, T.E. Runčevski, M.T. Kapelewski, B.K. Keitz, J.
Oktawiec, D.A. Reed, J.A. Mason, H.Z. Jiang, K.A. Colwell, C.M.
Legendre, J. Am. Chem. Soc. 138, 10143 (2016)
15. J. Reedijk, Proc. Natl. Acad. Sci. 100, 3611 (2003)
16. N.J. Wheate, J.G. Collins, Coord. Chem. Rev. 241, 133 (2003)
17. B. Lippert, Cisplatin: Chemistry and Biochemistry of a Leading
Anticancer Drug (Wiley, Hoboken, 1999)
44. F. Keshavarz, D. Mohammad-Aghaie, Phys. Chem. Res. 3, 125
(2015)
45. R. Thomsen, M.H. Christensen, J. Med. Chem. 49, 3315 (2006)
46. Z. Amirghofran, M. Bahmani, A. Azadmehr, K. Javidnia, Neo-
plasma 53, 428 (2005)
47. J. Jaumot, R. Gargallo, Curr. Pharm. Des. 18, 1900 (2012)
48. S.S. Bhat, A.A. Kumbhar, H. Heptullah, A.A. Khan, V.V. Gobre,
S.P. Gejji, V.G. Puranik, Inorg. Chem. 50, 545 (2010)
49. M. Sirajuddin, S. Ali, A. Haider, N.A. Shah, A. Shah, M.R. Khan,
Polyhedron 40, 19 (2012)
18. M. Roy, S. Roy, K.S. Singh, J. Kalita, S.S. Singh, New J. Chem.
40, 1471 (2016)
19. N. Sträter, W.N. Lipscomb, T. Klabunde, B. Krebs, Angew. Chem.
Int. Ed. 35, 2024 (1996)
50. M. Sirajuddin, S. Ali, N.A. Shah, M.R. Khan, M.N. Tahir, Spec-
trochim. Acta A Mol. Biomol. Spectrosc. 94, 134 (2012)
51. M.T. Carter, M. Rodriguez, A.J. Bard, J. Am. Chem. Soc. 111,
8901 (1989)
20. Q. Wang, H. Lönnberg, J. Am. Chem. Soc. 128, 10716 (2006)
21. A.K. Dhara, U.P. Singh, K. Ghosh, Inorg. Chem. Front. 3, 1543
(2016)
22. E. Hough, L.K. Hansen, B. Birknes, K. Jynge, S. Hansen, A.
Hordvik, C. Little, E. Dodson, Z. Derewenda, Nature 338, 357
(1989)
52. G.-J. Chen, X. Qiao, C.-Y. Gao, G.-J. Xu, Z.-L. Wang, J.-L. Tian,
J.-Y. Xu, W. Gu, X. Liu, S.-P. Yan, J. Inorg. Biochem. 109, 90
(2012)
23. J.B. Vincent, M.W. Crowder, B. Averill, Trends Biochem. Sci. 17,
105 (1992)
53. M. Sirajuddin, S. Ali, A. Badshah, J. Photochem. Photobiol. B,
Biol. 124, 1 (2013)
24. B.L. Vallee, D.S. Auld, Biochemistry 32, 6493 (1993)
25. J. Weston, Chem. Rev. 105, 2151 (2005)
54. M. Niu, Z. Li, H. Li, X. Li, J. Dou, S. Wang, RSC Adv. 5, 37085
(2015)
26. R. Sanyal, X. Zhang, P. Kundu, T. Chattopadhyay, C. Zhao, F.A.
Mautner, D. Das, Inorg. Chem. 54, 2315 (2015)
55. E. Sundaravadivel, S. Vedavalli, M. Kandaswamy, B. Varghese,
P. Madankumar, RSC Adv. 4, 40763 (2014)
27. T. Koike, E. Kimura, J. Am. Chem. Soc. 113, 8935 (1991)
28. R. Sanyal, A. Guha, T. Ghosh, T.K. Mondal, E. Zangrando, D.
Das, Inorg. Chem. 53, 85 (2013)
56. N. Shahabadi, S. Kashanian, F. Darabi, DNA Cell Biol. 28, 589
(2009)
57. F. Samari, B. Hemmateenejad, M. Shamsipur, M. Rashidi, H.
Samouei, Inorg. Chem. 51, 3454 (2012)
29. P. Molenveld, W.M. Stikvoort, H. Kooijman, A.L. Spek, J.F. Eng-
bersen, D.N. Reinhoudt, J. Org. Chem. 64, 3896 (1999)
30. G. Barone, A. Terenzi, A. Lauria, A.M. Almerico, J.M. Leal, N.
Busto, B. García, Coord. Chem. Rev. 257, 2848 (2013)
31. K. Selmeczi, C. Michel, A. Milet, I. Gautier-Luneau, C. Philouze,
J.L. Pierre, D. Schnieders, A. Rompel, C. Belle, Chem. Eur. J. 13,
9093 (2007)
58. Y. Sun, S. Bi, D. Song, C. Qiao, D. Mu, H. Zhang, Sens. Actuators
B Chem. 129, 799 (2008)
59. M. Khorasani-Motlagh, M. Noroozifar, A. Moodi, S. Niroomand,
J. Photochem. Photobiol. B, Biol. 127, 192 (2013)
60. M. Anjomshoa, H. Hadadzadeh, M. Torkzadeh-Mahani, S.J.
Fatemi, M. Adeli-Sardou, H.A. Rudbari, V.M. Nardo, Eur. J. Med.
Chem. 96, 66 (2015)
32. X. Zhang, X. Xu, H. Xu, X. Zhang, D.L. Phillips, C. Zhao,
ChemPhysChem 15, 1887 (2014)
61. G. Zhang, X. Hu, N. Zhao, W. Li, L. He, Pestic. Biochem. Physiol.
98, 206 (2010)
33. P. Joshi, N. Hussain, S.R. Ali, V.K. Bhardwaj, New J. Chem. 42,
2204 (2018)
62. F. Jalali, G. Rasaee, Int. J. Biol. Macromol. 81, 427 (2015)
63. T. Sarwar, S.U. Rehman, M.A. Husain, H.M. Ishqi, M. Tabish,
Int. J. Biol. Macromol. 73, 9 (2015)
34. R. Brissos, D. Ramos, J.C. Lima, F.Y. Mihan, M. Borras, J. de
Lapuente, A. Dalla Cort, L. Rodríguez, New J. Chem. 37, 1046
(2013)
64. K. Zheng, L. Zhu, Y.-T. Li, Z.-Y. Wu, C.-W. Yan, J. Photochem.
Photobiol. B, Biol. 149, 129 (2015)
35. M. Asadi, Z. Asadi, S.B. Sadi, L. Zarei, F.M. Baigi, Z. Amirg-
hofran, Spectrochim. Acta A Mol. Biomol. Spectrosc. 122, 118
(2014)
65. M. Waring, J. Mol. Biol. 13, 269 (1965)
66. J.M. Kelly, A.B. Tossi, D.J. McConnell, C. OhUigin, Nucleic
Acids Res. 13, 6017 (1985)
36. M. Asadi, Z. Asadi, L. Zarei, S.B. Sadi, Z. Amirghofran, Spectro-
chim. Acta A Mol. Biomol. Spectrosc. 133, 697 (2014)
37. U.M. Raf, D. Mahendiran, A.K. Haleel, R.P. Nankar, M. Doble,
A.K. Rahiman, New J. Chem. 40, 2451 (2016)
67. J. Liu, H. Zhang, C. Chen, H. Deng, T. Lu, L. Ji, Dalton Trans.
114 (2003)
68. S.E.H. Etaiw, D.M.A. El-Aziz, E.H.A. El-Zaher, E.A. Ali, Spec-
trochim. Acta, Part A 79, 1331 (2011)
38. M. Bheemarasetti, K. Palakuri, S. Raj, P. Saudagar, D. Ganda-
malla, N.R. Yellu, L.R. Kotha, J. Iran. Chem. Soc. 15, 1377 (2018)
39. A. Zarnegaryan, Z. Pahlevanneshan, M. Moghadam, S. Tangesta-
ninejad, V. Mirkhani, I. Mohammdpoor-Baltork, J. Iran. Chem.
Soc. 16, 747 (2019)
69. R. Mladenova, M. Ignatova, N. Manolova, T. Petrova, I. Rashkov,
Eur. Polym. J. 38, 989 (2002)
70. O. Walsh, M. Meegan, R. Prendergast, T. Al Nakib, Eur. J. Med.
Chem. 31, 989 (1996)
40. A.M. Abu-Dief, I.M. Mohamed, Beni-suef university journal of
basic and applied sciences 4, 119 (2015)
71. Z.-Y. Yang, R.-D. Yang, F.-S. Li, K.-B. Yu, Polyhedron 19, 2599
(2000)
41. Z. Asadi, M. Golchin, V. Eigner, M. Dusek, Z. Amirghofran,
Inorg. Chim. Acta 465, 50 (2017)
72. X. Zhong, J. Yi, J. Sun, H.L. Wei, W.S. Liu, K.B. Yu, Eur. J. Med.
Chem. 41, 1090 (2006)
42. C. N. Verani, E. Rentschler, T. Weyhermüller, E. Bill, P. Chaud-
huri, J. Chem. Soc. Dalton Trans. 251 (2000)
43. M.A. Lie, R. Thomsen, C.N. Pedersen, B. Schiøtt, M.H. Chris-
tensen, J. Chem. Inf. Model. 51, 909 (2011)
1 3