S. De and S.K. Ashok Kumar
Inorganic Chemistry Communications 119 (2020) 108085
calculated according to the equation (iv)
plate. The entire cell lines was cultured in 100 μL of a growth medium
in 96-well plates and incubated at 37 °C under 5% CO overnight. After
2
I
I
R
S
OD
OD
S
R
S
24 h of incubation, the cultured cells were exposed to various con-
centrations of the ligands (S1-S5) (9–300 µM). After 24 h, the wells
were treated with 10 μL MTT reagent (1 mg/ml) and incubated for 3 h
at 37 °C. The suspension was retained on micro vibrator for 10 min and
afterward the absorbance was calculated by the ELISA reader at λmax
(570 nm). The testing was executed in triplicate. The growth inhibition
percentage was calculated according to the equation [33–35]: percen-
tage growth inhibition = 100-[(AD × 100)/AB], where AD, measured
absorbance in wells which contain samples and AB, measured absor-
bance for blank wells.
R
R
(iv)
where, φ, I, OD, and η represents quantum yield, peak area, absorbance
recorded at λmax, and refractive index of solvent respectively.
The interaction of ligand with BSA has been calculated from tryp-
tophan fluorescence quenching response [26]. Here, the ligand solution
was incrementally added to BSA in Tris-HCl-NaCl buffer at pH 7.2. The
SV quenching constant (KBSA) of the fluorescence at 340 nm was cal-
culated using equation (v and vi). Further, using Scatchard equation
(
vii), K and n values were calculated [27].
I
I
0
q 0
[Q]
2
.5. In-silico study and DFT theory
(v)
KBSA
In order to know molecular interactions, each ligand was in-
0
(vi)
vestigated for their binding affinities by molecular docking study using
Autodock vina [36] along with the features of AutoDock Tools (ADT).
In search of a smaller DNA section [d(CCGTCGACGG], an widely used
leton of all five synthesized compounds (S1-S5) were developed using
ACD ChemSketch Freeware. Further, 3D coordinates structures were
built to make these fit to get into the subsequent stages of docking [39].
The binding site was mapped with a grid box with a spacing of 1 Å and
24 × 24 × 24 number of points was used in x y and z directions. Both
the target and the compounds were tuned to introduce their pdbqt
forms. The process yielded 9 poses for each ligand by considering the
exhaustiveness of 8. Two aspects, via the scoring functions and close
proximity between the conformer and active site residues were con-
sidered to assess the quality of all the bioactive conformers. Several
orientations of each compound within the active site were observed
using PyMOL (The PyMOL Molecular Graphics System, Version 1.3,
Schrodinger, LLC) molecular graphics program. In an attempt to de-
velop the virtual understanding of protein binding study and subse-
quently correlating it with the experimental study, molecular docking
study was conducted with the 3D structure of BSA with PDB ID: 4F5S
[40]. The protein structure was made free from water molecule so as to
avoid the probability of undesired interaction. The other process was
followed as similar as that of the earlier one. The grid box was placed
considering the relative positions of two essential active site residues,
via. Trp213 and Trp134 [41].
I0
I
log
I
(vii)
where, I
0
, I , k
q
, τ , K and n represents emission intensities of BSA in the
0
absence and in the presence of quencher of concentration [Q],
−
8
quenching constant, average lifetime of tryptophan (1 × 10
binding constant and number of binding sites respectively [28].
s),
2
.2. Relative viscosity study
To find out the type of binding interaction of S1-S5 with DNA was
studied by viscosity measurements using Ostwald’s viscometer. Each
experiment was performed for three times and the average flow time
1
/3
was recorded. The data was plotted as (η/η
0
)
vs. [ligand]/[DNA],
where η and η
ligand, and viscosity of DNA alone respectively. The viscosity of DNA
was calculated using the formula η = (t-t )/t where t and t re-
presents the efflux time of DNA and PBS buffer solution respectively
29–31].
0
corresponds to viscosity of DNA in the presence of the
0
0
0
0
[
2
.3. DNA degradation study
Initially, 0.15 g of plasmid DNA (~1 kb) was dissolved in 1 mL of
Tris-HCl-NaCl buffer solution and further this solution was mixed with
an equal volume of ligand (containing 1, 2 and 3 mg/ml). This solution
mixture was incubated for 1 h at 37 °C and loaded on 1% agarose gel
containing EtBr (1.0 mg/ml) and 2 mL buffer solution (containing 25%
bromophenol blue, 30% glycerol and 0.25% xylene cyanol). Here,
plasmid DNA was used as a positive control. The degradation experi-
ment was carried out at 50 V for 60 min in buffer solution [32] and the
gel plate was visualized using a gel documentation instrument.
To calculate electronic properties of ligand, computational calcu-
lations was performed in the gas phase using density functional theory
(DFT) by applying the Becke three-parameter Lee-Yang-Parr (B3LYP)
exchange correlation functional. The basic set 6-311G(d,p) was used for
all atoms. All the geometrical optimizations were done with zero ne-
gative vibrational frequency. The calculations were carried out using
Gaussian 09 program [42].
2
.4. In-vitro cytotoxic study
3
. Results and discussion
Each ligand was dissolved in 0.1% DMSO and then serial dilution
with cell medium. Here, we have selected two different cancer cell lines
such as HeLa, MDA-MB-231 and normal cell lines HEK-293 were used
in this assay. The doxorubicin was used as a positive control with the
same volume of medium. Hemocytometer was used for counting of
3.1. Synthesis and photo-physical studies of ligands
The synthesis of ligand S5 follows four steps reaction via various
intermediates such as 1,10-phenanthroline-2,9-dicarbaldehyde (S2),
1,10-phenanthroline-2,9-dicarboxylic acid (S3), 1,10-phenanthroline-
4
cells. The amount of cell seeded was 1 × 10 cells per well in a 96 well
HNO3
MeOH
SeO2
NH -NH H O
2
2. 2
H SO
N
N
Dioxane
N
N
2
4
N
N
N
N
N
N
MeOH
HN
H N
NH
NH2
HO
OH
O
O
O
O
O
O
O
O
O
O
2
Scheme 1. Reagents and conditions to synthesize ligands S2-S5.
3