Novel functionalized thiosemicarbazone ligands and their Pd(II) complexes: synthesis, characterization, antibacterial and cytotoxic activities

Article abstract of DOI:10.1007/s11696-018-0592-6

Palladium (II) complexes of coumarinyl thiosemicarbazone derivatives as 1-(1-(2-oxo-2H-chromen-3-yl) ethylidene) thiosemicarbazone (OCETh), 1-(1-(6-bromo-2-oxo-2H-chromen-3-yl) ethylidene) thiosemicarbazone (BOCETh) and 1-(1-(3-oxo-3H-benzo[f]chromen-2-yl)ethylidene) thiosemicarbazone (NOCETh) were prepared. The complexes have the formula [Pd (L) Cl]. DMF, where DMF = dimethylformamide and L = OCETh, BOCETh or NOCETh. The studied ligands act as a tridentate ligand by using azomethine nitrogen, carbonyl oxygen and thiol sulfur as a monoanion center of donation. The characterization part was carried out using different physicochemical tools such as elemental analysis, IR, UV–visible, mass, magnetic measurement and molar conductance techniques. The theoretical conformational structure analyses were performed using density functional theory for ligands and complexes at B3LYP functional with 6–31 ++G(d,p) basis set for ligands and LANL2DZ basis set for complexes. The charge distribution within the ligands and its pd(II) complexes was calculated using Mulliken population analysis of (MPA) and natural population analysis (NPA). The prepared pd(II) complexes showed a satisfactory cytotoxic effect results against the human colon cancer cell line (HCT-116). Additionally, docking study was performed on colon cancer target cyclin-dependent kinase-2 to understand the cytotoxic modes of actions by the active compounds. The antibacterial activity was tested against some types of Gram-positive and negative bacteria. Molecular docking investigation proved that all synthesized compounds had interesting interactions with the active site amino acids of glucosamine-6-phosphate synthase. Density functional theory was used to theoretically analyze the conformational structure of the ligands and Pd (II) complexes.

Full text of DOI:10.1007/s11696-018-0592-6

Chemical Papers
https://doi.org/10.1007/s11696-018-0592-6
ORIGINAL PAPER
Novel functionalized thiosemicarbazone ligands and their Pd(II)
complexes: synthesis, characterization, antibacterial and cytotoxic
activities
Safaa S. Hassan1 · Sobhi M. Gomha1
Received: 12 April 2018 / Accepted: 11 September 2018
©
Institute of Chemistry, Slovak Academy of Sciences 2018
Abstract
Palladium (II) complexes of coumarinyl thiosemicarbazone derivatives as 1-(1-(2-oxo-2H-chromen-3-yl) ethylidene) thiosem-
icarbazone (OCETh), 1-(1-(6-bromo-2-oxo-2H-chromen-3-yl) ethylidene) thiosemicarbazone (BOCETh) and 1-(1-(3-oxo-
3
H-benzo[f]chromen-2-yl)ethylidene) thiosemicarbazone (NOCETh) were prepared. The complexes have the formula [Pd
(
L) Cl]. DMF, where DMF = dimethylformamide and L = OCETh, BOCETh or NOCETh. The studied ligands act as a
tridentate ligand by using azomethine nitrogen, carbonyl oxygen and thiol sulfur as a monoanion center of donation. The
characterization part was carried out using diꢀerent physicochemical tools such as elemental analysis, IR, UV–visible, mass,
magnetic measurement and molar conductance techniques. The theoretical conformational structure analyses were performed
using density functional theory for ligands and complexes at B3LYP functional with 6–31 ++G(d,p) basis set for ligands
and LANL2DZ basis set for complexes. The charge distribution within the ligands and its pd(II) complexes was calculated
using Mulliken population analysis of (MPA) and natural population analysis (NPA). The prepared pd(II) complexes showed
a satisfactory cytotoxic eꢀect results against the human colon cancer cell line (HCT-116). Additionally, docking study was
performed on colon cancer target cyclin-dependent kinase-2 to understand the cytotoxic modes of actions by the active
compounds. The antibacterial activity was tested against some types of Gram-positive and negative bacteria. Molecular
docking investigation proved that all synthesized compounds had interesting interactions with the active site amino acids of
glucosamine-6-phosphate synthase. Density functional theory was used to theoretically analyze the conformational structure
of the ligands and Pd (II) complexes.
Keywords Coumarin-yl thiosemicarbazone derivatives · Pd(II) complexes · Glucosamine-6-phosphate synthase · HCT-
1
16 · Cyclin-dependent kinase-2
Introduction
drugs, but also to search for new drug targets. In case of anti-
bacterial drug discovery, bacterial proteins are the ultimate
target to inhibit their growth since these are the executors
of many cellular functions (Nawrot-Modranka et al. 2006).
The synthesis of glucosamine-6-phosphate (GlcN-6-P) was
done by using glucosamine-6-phosphate synthase enzyme
from d-l-glutamine and fructose-6-phosphate. The enzyme
is responsible for the ꢁrst stage of the formation of UDP-N-
acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is present
in all types of organisms (Tyagi and Chandra 2012; Li et al.
Colorectal cancer is the fourth most commonly diagnosed
malignant disease. It is the second most common cancer
in women and the third in men (Mulwad and Pawar 2003;
Sharma and Pritmani 1999). Also, bacterial infection is
considered one of the most important diseases worldwide.
Thus, it is urgently needed not only to improve the existing
*
Safaa S. Hassan
2
006; Deming et al. 2014). The eꢀect of inactivation time of
Safaa_inorgchem@yahoo.com
the GlcN-6-P synthase in microbes is diꢀerent from that in
human cells. Its depletion in bacteria is lethal for the patho-
gen because of the morphological changes, agglutination
and lysis; however in the case of mammals, the depletion of
the amino sugar pool for a short time is not lethal due to the
Sobhi M. Gomha
s.m.gomha@gmail.com
1
Department of Chemistry, Faculty of Science, Cairo
University, Giza, Egypt
Vol.:(0
1
123456789)
3

Chemical Papers
long half-life time of the GlcN-6-P synthase and the rapid
expression of the mammalian gene encoding this enzyme
Experimental
(
Huang et al. 2014; Vidya et al. 2012; Bates and Pasternak
Palladium (II) chloride salt and all other chemicals were
purchased from Sigma Company.
1
965). Also, in case of cancer resistance, blocking of the
oncogenic activation in cancer cells by using of tyrosine
kinase inhibitors is an important target in ꢁghting cancer
cells, because tyrosine kinases in the diverse biological pro-
cesses are an important mediator.
Preparation of ligands and their pd(II) complexes
Schiꢀ base ligands (L)
Coumarin derivatives are important sources of heterocy-
clic compounds of pharmocological interest, as they show
a wide spectrum of biological activities (Gomha and Khalil
1-(1-(2-Oxo-2H-chromen-3-yl) ethylidene) thiosemicarba-
zone (OCETh), 1-(1-(6-bromo-2-oxo-2H-chromen-3-yl) eth-
ylidene) thiosemicarbazone (BOCETh) and 1-(1-(3 s-oxo-
3H-benzo[f]chromen-2-yl) ethylidene) thiosemicarbazone
(NOCETh) were prepared according to the known condensa-
tion method (Fessenden and Fessenden 1990).
2012; Pavurala and Vedula 2015; Shruthi et al. 2012; Suzuki
et al. 2003; Weigt et al. 2012). In particular, the antitumor
activity of coumarin compounds has received considerable
attention among researchers because of their cytotoxic activ-
ity against numerous types of cancers, including malignant
melanoma, leukemia, renal cell carcinoma, prostate and
breast cancer cell progression (Gomha et al. 2015; Musa
et al. 2011; Steꢀen et al. 1998).
[Pd(L)(Cl)](DMF) complexes
Pd(II) complexes were synthesized by heating PdCl
2
It is well known that the cooperation between many
metal ions improves the biological activities of thiosemi-
carbazone, especially platinum group metals (Chmara and
Borowski 1986; Cutillas et al. 2013; Kapdi and Fairlamb
(
0.1773 g; 1.0 mmol) and KCl (0.149 g; 2.0 mmol) in the
least amount of water to 70 °C with stirring. The clear solu-
2
−
tion of [PdCl ] solution was cooled to 25 °C, ꢁltered and
4
mixed with a solution of each thiosemicarbazone ligand
2
014; Pranczk et al. 2014). Palladium is one of these met-
(
1.0 mmol, in 5 mL DMF) with a molar ratio 1:1 (Pd:L).
als whose complexes exhibit a noticeable cytotoxic activ-
ity similar to the standard platinum-based drug references
such as cisplatin, carboplatin and oxaliplatin, with fewer side
eꢀects relative to other heavy metal anticancer compounds
Brownish orange complexes were precipitated, filtered,
washed and ꢁnally dried under vacuum.
1
The output data of elemental, IR and HNMR characteri-
zation of the synthesized ligands and their Pd(II) complexes
are mentioned in Tables 1, 2 and 3.
(
Milewski et al. 1986). So, the complexes formed due to
the combination between the coumarinyl thiosemicarbazone
derivatives and pd(II) ion is expected to have high antibacte-
rial and antitumor eꢀects (Kokotos et al. 1997). Considering
all of the above, the aim of our work is to examine the eꢀect
of some novel Pd (II) complexes of coumarinyl thiosemicar-
bazone compounds as possible antibacterial and colon anti-
cancer agents with further rationalization of the biological
results by performing molecular docking on the synthesized
compounds to predict the best mode by which a compound
will ꢁt into a binding site of a macromolecular target.
Characterization analyses
All characterization analyses were done at the Microana-
lytical Center, Cairo University, Giza, Egypt. The elemental
analysis was done by using CHN automatic analyzer Vario
EL III–Elementar, Germany. IR spectra were recorded using
−
1
Shimadzu FTIR spectrometer in the range 200–4000 cm .
The molar magnetic susceptibility measurement of the Pd
(II) complexes was measured using a magnetic suscepti-
bility Cambridge, England Sherwood Scientiꢁc at room
Table 1 Analytical and physical data of (OCETh), (BOCETh), (NOCETh) and their Pd(II) complexes
Compound empirical formula
Molecular weight
Color
Yield
Found (Calc.) %
C
H
N
(
OCETh) C H N O S
261.3
475.26
340.2
554.15
311.36
525.32
Yellowish cream
Dark orange
Yellowish cream
Dark orange
Yellowish cream
Dark orange
80%
80%
80%
80%
54.16 (55.16)
36.99 (37.91)
41.0 (42.37)
31.90 (32.51)
61.20 (61.72)
43.0 (43.44)
4.0 (4.24)
2.99 (3.61)
2.5 (2.96)
2.35 (2.91)
3.95 (4.21)
3. 0 (3.65)
15.3 (16.08)
11.10 (11.79)
12.1 (12.35)
9.78 (10.11)
12.9 (13.5)
12
11
3
2
Pd[(C1 H N O S) Cl].DMF
2
10
3
2
(
BOCETh) C H BrN O S
12
10
3
2
Pd[(C H BrN O S) Cl].DMF
12
9
3
2
(
NOCETh) C H N O S
16
13
3
2
Pd[(C H N O S)Cl].DMF
80%
10.1 (10.67)
16
12
3
2
1
3

Chemical Papers
Table 2 Infrared spectral data of [(OCETh), (BOCETh) and (NOCETh)] and their Pd(II) complexes (cm−1
)
Compound
υ (NH2) υ (=C–H) υ (–C–H) υ (C=O) υ (C–H)ald. υ (C=N) υ (Pd–N) υ (Pd–O) υ (Pd–S) υ (Pd–Cl)
aromatic
(
OCETh)
3388
3319
3153
3145
3044
2957
1719
1652
–
2925
1603
–
508
–
473
–
367
–
343
Pd–OCETh
1598
1
642
1551
(
BOCETh)
3405
3377
3135
3072
2985
3051
1723
1653
–
2925
1590
–
552
–
470
–
365
–
349
Pd–BOCETh
1595
1
649
1551
(
NOCETh)
3404
3380
3154
3150
2946
2957
1714
1637
–
2925
1593
–
526
–
449
–
360
–
346
Pd–NOCETh
1578
1
647
1550
1
Table 3 HNMR output of
Compound
OCETh)
Pd–OCETh
BOCETh)
Pd–BOCETh
NOCETh)
Pd–NOCETh
δ (5H, Ar.)
δ (3H, methyl)
δ (H, NH)
δ (2H, NH2)
δ (1H, CHO)
[
(
(OCETh), (BOCETh) and
NOCETh)] and their pd(II)
(
7.36–7.97
6.65–7.66
7.38–7.97
6.99–7.72
7.40–7.97
7.40–8.90
3.37
3.52
3.28
3.56
3.41
3.40
10.48
–
10.42
–
10.54
–
8.43
8.65
8.40
8.60
8.48
9.49
–
complexes (ppm)
10.25
–
10.21
–
(
(
10.79
temperature. The eꢀective magnetic moments were cal-
plates. 10 μl of the testing concentration was spotted into
blank paper disks (Schleicher & Schuell, Spain) with a diam-
eter of 8.0 mm and placed on agar media. The bacteria were
incubated at 35–37 °C for 24–48 h and then the diameters of
the inhibition zones were measured in millimeters (National
Committee for Clinical Laboratory Standards 2002).
1
/2
culated from the expression μ = 2.828(X T) B.M.,
eff
M
where X is the molar susceptibility corrected using Par-
M
cel’s constants for diamagnetism of all atoms in the com-
pounds (Emeleus and Sharpe 1974). UV/Vis-NIR 3101 PC
Shimadzu spectrophotometer ranging from 200 to 900 nm
was used for the measurement of the electronic absorption
1
spectra in DMSO as a solvent. The H NMR spectra were
recorded on a Varian (300 MHz) spectrometer. The molar
conductivity of the synthesized Pd (II) complexes was meas-
−
3
ured by the preparation of solutions with 10 M concentra-
tion with DMF as a solvent, using the conductivity meter
ORION model 150 with 0.6 cells constant. Mass GC-2010
Shimadzu instrument was used to determine the mass spec-
tra of the synthesized complexes.
Table 4 UV–Vis spectral data of [(OCETh), (BOCETh) and
(
NOCETh)] and their Pd(II) complexes
Compound
OCETh
λmax (nm)
Assignment
258
П–П*
n–П*
Biological measurements
3
49
BOCETh
NOCETh
Pd–OCETh
267
П–П*
The antibacterial activity of the ligands and their Pd (II)
complexes was determined using the modiꢁed Kirby–Bauer
disc diꢀusion method (National Committee for Clinical
Laboratory Standards 2002). 100 μl of the test bacteria,
Gram (+) bacteria such as Bacillus subtilis and Staphylo-
coccus aureus and Gram (−) bacteria such as Pseudomonas
aeruginosa and Escherichia coli were grown in 10 mL
of Mueller–Hinton media until they reached a count of
357
n–П*
265
П–П*
n–П*
3
78
−
−
−1
1
1
1
1
242 [41,322 cm
]
]
]
Alg to B
1g
1g
2g
2
7
55 [39,215 cm
31 [13,679 cm
−1
−1
1
1
1
Pd–BOCETh
Pd–NOCETh
253 [39,525 cm
]
]
]
]
]
]
Alg to B
l
3
47 [28,818 cm
A
to E
lg
g
−1
733 [13,642 cm
245 [40,816 cm
7
−1
lA to A
l
approximately 10 cells/mL for bacteria (National Commit-
1
g
−1
4
7
12 [24,271 cm
tee for Clinical Laboratory Standards 2003) using the plate
counter. We spread the microbial suspension onto the agar
32 [13,661 cm−
1
1
3

Chemical Papers
Fig. 1 a Mass spectra of the Pd[(C H N O S)Cl].DMF complex. b Mass spectra of the Pd[(C H BrN O S)Cl].DMF complex. c Mass spectra
1
2
10
3
2
12
9
3
2
of the Pd[(C H N O S)Cl].DMF complex
16
12
3
2
Antitumor measurements
sulfonic groups) assay. SRB is a protein stain that attaches
to the amino groups of intracellular proteins under mildly
acidic conditions to provide a sensitive index of cellular
protein content. The cells were seeded in 96-well microti-
The cytotoxicity of the suggested Pd (II) drugs was deter-
mined by Vichai and Kirtikara (2006) using Sulforhoda-
mine-B (SRB is a bright pink aminoxanthrene dye with two
3
ter plates at an initial concentration of 3×10 cell/well in a
1
3

Chemical Papers
Me
O
150 µl fresh medium and left for 24 h to attach to the plates.
Five diꢀerent concentrations 0, 5, 12.5, 25, and 50 µg/mL
of the drug was added. For each drug concentration, three
wells were used. The plates were incubated for 48 h. The
cells were ꢁxed with 50 μl cold trichloroacetic acid of 10%
H
N
N
H
O
N
S
ꢁ
nal concentration for 1 h at 4 °C. Automatic washer Tecan,
Pd
Cl
O
Germany, was used to wash the plates with distilled water.
At room temperature, the plates were stained with 50 μl
N
Me
Me
0
.4% SRB dissolved in 1% acetic acid for 30 min. An ELISA
[
Pd(L)(Cl)]DMF
microplate reader (Sunrise Tecan reader, Germany) was used
to measure each well spectrophotometrically at 570 nm. The
mean value of the background absorbance was automatically
subtracted and the drug concentration was calculated. Each
L= OCETh, BOCETh or NOCETh
Fig. 2 The suggested structure of Pd (II) complexes
Fig. 3 (OCETh, BOCETh and NOCETh) ligands and their Pd(II) complex optimization geometry
Table 5 Ground state properties, HOMO–LUMO energy, hardness, dipole moment, ionization energy and electron aꢂnity of the OCETh,
BOCETh and NOCETh using B3LYP/6–31G(++)d,p and Pd(II) complexes using B3LYP/LANL2DZ
Parameter
OCETh
Pd[(OCETh)Cl] BOCETh
Pd[(BOCETh) Cl] NOCETh
Pd[(NOCETh)Cl]
ET, Hartree
EHOMO, Hartree
ELUMO, Hartree
− 1176.8214 − 1178.2408
− 3747.9488 − 1190.7933
− 1330.4745 − 1331.8612
− 0.21305
− 0.08797
3.4036
− 0.20484
− 0.11610
2.4147
− 0.21956
− 0.09645
3.3499
1.6749
3.1735
− 0.20939
− 0.12308
2.34861
1.17430
6.9968
− 0.21775
− 0.09173
3.429 18
1.7145
− 0.20284
− 0.11588
2.36630
1.18315
8.8132
E* , eV
g
Hardness=1/2 (E LUMO- E HOMO
µ, Dipole moment (Debye)
I.E=- E HOMO, eV
)
1.7018
1.2073
4.2375
0.21305
0.08797
8.1396
0.20484
0.11610
4.9090
0.21956
0.09645
0.20939
0.12308
0.21775
0.09173
0.20284
0.11588
EA=- E LUMO, eV
*
Eg=Diference between HOMO and LUMO
1
3

Chemical Papers
Table 6 Some of the optimized
bond length, Å and bond
angles, degrees, for OCETh,
BOCETh and NOCETh using
B3LYP/6-31G(++)d,p and
Pd(II) complexes using B3LYP/
LANL2DZ
Bond length (Ao)
OCETh
1.77601
1.31172
Pd-OCETh
BOCETh
Pd-BOCETh
NOCETh
Pd-NOCETh
C24–S28
C24–N23
N22–N23
C17–N22
C24–N25
C2–O16
N25–H 26
N25–H
O31(DMF)–H26
O31(DMF)–C32
C3–C17
Pd–S28
Pd–O16
Pd–Cl30
Pd–N22
1.81315
1.34388
1.38780
1.33820
1.35448
1.25209
1.02598
1.01226
1.75834
1.25859
1.47586
2.33244
2.08633
2.37191
2.07078
1.77462
1.31148
1.36153
1.29610
1.36047
1.20761
1.01039
1.00789
–
1.81220
1.34534
1.38593
1.33954
1.35355
1.25089
1.02648
1.01237
1.75266
1.25867
1.47477
2.33150
2.09078
2.36992
2.06981
1.78491
1.29928
1.37484
1.29726
1.36863
1.21186
1.01172
1.00937
–
1.81251
1.34345
1.38851
1.33888
1.35505
1.25347
1.02565
1.01216
1.76322
1.25845
1.47470
2.33237
2.08850
2.37220
2.06961
1.36212
1.29579
1.35671
1.20878
1.00895
1.00629
–
–
–
–
1.47641
1.47591
–
–
–
–
1.48242
–
–
–
–
–
–
–
–
Bond angles (Deg.)
S28–C24–N23
N23–N22–C17
N22–C17–C3
N22–Pd29–S28
N22–Pd29–Cl30
S28–Pd29–Cl30
N22–Pd29–O16
O16–Pd29–Cl30
125.676
118.698
117.481
–
–
–
–
125.319
115.564
123.915
86.799
176.558
89.762
91.025
92.412
125.821
118.538
117.428
–
–
–
–
–
125.301
115.520
123.953
86.892
176.705
89.813
91.032
92.263
126.201
116.111
115.190
–
–
–
–
–
125.289
115.538
123.825
86.823
176.657
89.835
91.224
92.118
experiment was repeated three times. The cell survival per-
cent was calculated by:
Results and discussion
Surviving fraction = optical density (O. D.) (treated
cells)/O. D. (control cells). The IC values (the concentra-
Investigation of ligands and their donation sites
to the Pd(II) ion
5
0
tions of resveratrol required to produce 50% inhibition of
cell growth) were also calculated.
(CHN) analyses for (OCETh, BOCETh and NOCETh)
ligands and their Pd (II) complexes showed a satisfactory
agreement between the experimental and theoretical results.
The analytical data are summarized in Table 1. The stoichio-
metric ratio of the synthesized complexes is 1:1 (Pd (II):
ligand).
Computational methods
GaussView 5.0.8 (Wallingford CT 2009a, b) was used to
visualize (OCETh), (BOCETh), (NOCETh) and their Pd (II)
complexes. DFT/B3LYP method was selected for all calcula-
tions using Gaussian 09 rev. A.02 (Wallingford CT 2009a,
b). The standard basis sets for the synthesized ligands and
their pd(II) complexes are 6–31++G(d,p) and LANL2DZ,
respectively. MOE 2008 (Molecular Operating Environment)
software was used to simulate every enzyme inhibitor. The
protein crystal structure of the protein GlcN-O-P synthase
1
Conductance, infrared, HNMR, magnetic, electronic
and spectral studies
The coordination sites for the complexes were conꢁrmed
by using the following observations. The infrared scanning
technique provided us the presence of thiol group vibra-
−
1
(
antimicrobial activity) (PDB ID: 1XFF) and EGFR tyrosine
tions at 2676–2649 cm and thione bands at 859, 827 and
−
1
kinase (anticancer activity) (PDB ID: 2R3 J) was obtained
from Protein Data Bank (PDB).
821 cm for the OCETh, BOCETh and NOCETh ligands,
respectively (Matesanz et al. 1999), indicating that they
remain as the thiol–thione tautomer forms. However, in the
case of the three pd(II) complexes, both types of vibrations
[
ν(SH) and ν(C=S)] were absent. It can be explained that the
coordination was done through the mononegatively charged
1
3

Chemical Papers
Table 7 Atomic charges in terms of MPA and NPA of Pd(II) complexes of OCETh, BOCETh and NOCETh using B3LYP/LANL2DZ and
ligands (OCETh), (BOCETh) and (NOCETh) using B3LYP/6-31G(++)d,p
Element
MPA
NPA
Pd–OCETh
Pd–BOCETh
(BOCETh)
Pd–NOCETh
(NOCETh)
Pd–OCETh
(OCETh)
Pd–BOCETh
(BOCETh)
Pd–NOCETh
(NOCETh)
(
OCETh)
Pd
O1
C2
C3
C4
C5
0.040 (–)
− 0.265 (− 0.379)
0.268 (0.578)
0.159 (0.476)
− 0.357 (0.261)
0.365 (0.968)
0.041 (–)
− 0.262 (− 0.409)
0.269 (0.736)
0.162 (0.931)
− 0.356 (0.323)
0.385 (0.017)
0.0392 (–)
0.291 (–)
− 0.511 (− 0.501)
0.832 (0.797)
− 0.174 (− 0.178)
− 0.128 (− 0.130)
− 0.124 (− 0.149)
0.291 (–)
0.292 (–)
− 0.261 (− 0.393)
0.259 (0.173)
0.163 (0.020)
− 0.338 (0.127)
0.211 (0.968)
− 0.510 (− 0.500) − 0.508 (− 0.502)
0.833 (0.797) 0.827 (0.774)
− 0.170 (− 0.172) − 0.174 (− 0.189)
− 0.132 (− 0.133) − 0.126 (− 0.097)
− 0.110 (− 0.134) − 0.105 (− 0.140)
C6
C7
C8
C9
C10
O16
C17
C18
N22
N23
C24
N25
S28
Cl30
0.156 (− 2.088)
− 0.322 (− 0.379)
− 0.191 (− 0.267)
− 0.233 (0.122)
− 0.378 (0.206)
− 0.277 (− 0.407)
0.263 (0.045)
− 0.765 (− 0.357)
− 0.249 (− 0.323)
− 0.113 (− 0.029)
− 0.096 (− 0.043)
− 0.607 (− 0.369)
0.107 (0.082)
0.154 (− 1.700)
− 0.311 (− 0.205)
− 0.117 (− 0.483)
0.142 (− 0.700) 0.354 (0.347)
0.351 (0.346)
− 0.214 (− 0.249) − 0.230 (− 0.262)
− 0.197 (− 0.220) − 0.152 (− 0.175)
0.372 (0.361)
− 0.358 (− 0.386)
− 0.425 (− 0.263)
− 0.229 (− 0.264)
− 0.180 (− 0.207)
− 0.214 (− 0.251) − 0.114 (− 0.138) − 0.058 (− 0.066)
− 0.277 (− 0.196) 0.427 (0.283)
− 0.279 (0.426)
− 0.276 (− 0.366)
0.263 (0.213)
− 0.765 (− 0.579)
− 0.249 (− 0.193)
− 0.111 (− 0.135)
− 0.095 (− 0.083)
− 0.605 (− 0.324)
0.111 (0.076)
0.234 (1.016)
− 0.173 (− 0.191)
− 0.544 (− 0.566)
0.287 (0.226)
− 0.689 (− 0.722)
− 0.274 (− 0.281)
− 0.433 (− 0.431)
0.331 (0.290)
− 0.793 (− 0.833)
− 0.032 (− 0.015)
− 0.396 (–)
− 0.193 (− 0.207) − 0.026 (− 0.019)
− 0.541 (− 0.560) − 0.549 (− 0.574)
0.285 (0.226)
− 0.689 (− 0.722) − 0.690 (− 0.709)
− 0.272 (− 0.279) − 0.275 (− 0.315)
− 0.429 (− 0.427) − 0.434 (− 0.422)
0.331 (0.289)
− 0.790 (− 0.831) − 0.795 (− 0.848)
− 0.026(− 0.008)
− 0.391 (–)
− 0.281 (− 0.419)
0.252 (− 0.220)
− 0.773 (− 0.489)
− 0.252 (− 0.290)
− 0.114 (− 0.115)
− 0.096 (− 0.018)
− 0.608 (− 0.350)
0.105 (0.059)
0.288 (0.255)
0.331 (0.281)
0.033 (− 0.008)
− 0.397 (–)
− 0.284 (–)
− 0.281 (–)
− 0.285 (–)
O31(DMF) − 0.340 (–)
− 0.341 (–)
0.0144 (–)
− 0.077 (–)
0.008(0.010)
− 0.339 (–)
− 0.712 (–)
0.557 (–)
− 0.468 (–)
– (–)
− 0.713 (0.074)
0.557 (–)
− 0.467 (–)
− 0.711 (–)
C32
N34
Br13
− 0.013 (–)
− 0.077 (–)
– (–)
0.013 (− 0.301)
− 0.078 (− 0.182)
– (–)
0.556 (− 0.223)
− 0.468 (− 0.238)
– (–)
0.073 (0.074)
Fig. 4 Pd(II) complexes molecular graphs of OCEhT, BOCETh and NOCETh, respectively
sulfur atom via deprotonation of the –SH group (Matesanz
et al. 1999). The vibration band of the azomethine (C=N)
group was shifted to a lower value by complexation, lead-
ing to the coordination of palladium ion by the azomethine
nitrogen. The band positions of the carbonyl groups of the
ligands changed after complexation to lower values, due to
the coordination of carbonyl oxygen with palladium ion in
the complexation process. The vibrational frequencies of the
optimized ligands and their palladium (II) complexes were
calculated and no imaginary frequencies were observed.
The complete neutralization of the complex was done by
the binding with one chloride ion that was supported by the
appearance of a new Pd–Cl band (Matesanz et al. 1999).
It is further supported by the non-electrolytic properties of
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Table 8 Antibacterial activity
data of (OCETh, BOCETh and
NOCETh) ligands and their
Pd(II) complexes, inhibition
zone (mm)
Sample
Inhibition zone diameter(mm/mg sample)
Escherichia coli Pseudo monas aerugi- Bacillus subtilis
Staphylococcus
aureus (G+)
(G-)
nosa (G-)
(G+)
Control: DMSO
0.0
14
15
12
12
9
0.0
13
17
10
13
0.0
10
0.0
13
15
11
13
0.0
11
0.0
14
16
10
12
0.0
11
(
[
(
[
(
[
OCETh)
Pd(OCETh)Cl]
BOCETh)
Pd(BOCETh)Cl]
NOCETh)
Pd(NOCETh)Cl]
10
Fig. 5 Biological activity of ligands and their Pd (II) complexes toward diꢀerent types of bacterial strains
the synthesized complexes (Nakamoto 1986). All previous
coordinated bond signals observed due to (Pd–N), (Pd–O),
Urbach 1969). The deuterated (D O) spectrum of each
2
examined ligand conꢁrmed the lability of NH proton by
its disappearance. The presence of DMF molecule as pre-
viously discussed in IR, was supported by the deuterated
(
Pd–S) and (Pd–Cl) (Melo et al. 1988) are shown in Table 2
with the most important characteristic bands. The well-
−1
resolved bands at 3199, 3147 and 3197 cm for Pd–OCETh,
Pd–BOCETh and Pd–NOCETh complexes, respectively
(D O) spectrum of each Pd(II) complex. The signal observed
2
at (10.21–10.79) did not disappear. This signal mainly cor-
(
Matesanz et al. 1999), may be assigned to strong intermo-
responds to the (1H, CHO) group and not the (H, NH) group
lecular hydrogen bonding between the terminal uncoordi-
with the downꢁeld shift in the value of NH group related to
2
nated amino groups (NH ) and the carbonyl oxygen atoms
the hydrogen bond formation.
2
(C=O) of the dimethylformamide molecule with a clear shift
All studied Pd (II) complexes are diamagnetic as predict-
8
in their stretching vibrations, knowing that the υ carbonyl
of the free DMF molecule equals 1670 (Hassan 2017). The
presence of DMF molecules is conꢁrmed by the appearance
of new bands of υ [C–H DMF] at 2925 in all complexes.
able for d system square planar with diamagnetic nature
(Melo et al. 1988). The electronic spectra results are shown
in Table 4. The bands of ligands at 258–267 nm (37, 453–38,
−1
759 cm ) are due to π–π* of the aromatic region. The bands
corresponding to n–π* for transition (C=S), (C=O) and
azomethine (C=N) (Mason and Gray 1968) groups of ligands
1
H NMR analysis conꢁrmed the coordination (Table 3)
via the deprotonation of the thiol tautomer and the forma-
tion of an intermolecular hydrogen bond as shown in the IR
discussion by the disappearance of the band corresponding
to the NH group and the clear shift of the terminal amino
group that is responsible for the hydrogen bonding forma-
tion after each Pd (II) complex formation (Downing and
−1
are found in the region 349–378 nm (26, 455–28, 653 cm ).
For Pd(II) complexes, the ꢁrst spin-allowed d–d transition
l
l
−1
A
to A is observed at 24,271 cm . The assignment of
2g
1
g
−
l
the band observed at 28, 818 cm corresponds to the transi-
l
1
tion A to Eg. The designation of the band is observed at
lg
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Chemical Papers
Fig. 6 The antibacterial docking results of (OCETh, BOCETh and NOCETh) ligands
−
1
1
1
about 39,000 cm , as the transition A – B is the least
lg
1g
ꢁ
rmly based on the spin-allowed assignments. However, the
−
1
Table 9 Comparison of binding aꢂnity of (OCETh, BOCETh and
NOCETh) ligands and their Pd(II) complexes against bacterial target
protein (PDB ID: 1XFF)
charge transfer bands appeared beyond 40,000 cm . The
−l
weaker bands at about 13,000 cm are logically assigned to
spin-forbidden d–d transitions. Thus, the electronic spectra
of these complexes are indicative of square planar geometry
Antibacterrial docking 1xꢀ
(
El-Gammal 2010).
Compound
Involved group of amino acid Length of H bond Å
OCETh
Thr-76
Thr-76
His-97
Tryp-74 and Cys-1
2.16
2.35
1.76
2.4 and 2.8
2.96
Mass spectra study
BOCETh
NOCETh
Pd–OCETh
Pd–BOCETh Gly-99
Pd–NOCETh Gly-99
Mass spectra of the Pd(II) complexes are proven and
declared in Fig. 1a–c. It supports the coordination modes
for the suggested structure geometries in Fig. 2.
2.1
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Chemical Papers
Fig. 7 The antibacterial docking results of Pd–OCETh, Pd–BOCETh and Pd–NOCETh complexes, respectively
Geometric study
to the comparable values of their energy gaps. The lower
energy gap leads to a higher reactivity of the complex.
From the calculated data in Table 6, many geometric
changes are observed in the studied ligands after complexa-
tion by increasing the bond lengths: C24–S28, C17–N22,
C24–N23, N22–N23 and C2–O16. Due to the formation of
the M–S, M–N and M–O bonds. C–S, C–N and C–O bonds
become weaker (Naseh et al. 2013). So, the bonding takes
place via the sulfur of the deprotonated thiol group, N atom
of the (C=N) azomethine (Hassan 2017; Hassan et al. 2017)
and the oxygen carbonyl group. N–H26 bond length of the
terminal amino group in the ligands is elongated due to the
formation of hydrogen bond with the DMF molecule. The
The geometric optimization of ligands and their pd(II) com-
plexes with the numbering system is seen in Fig. 3. The
values of energy, dipole moment, gap energy and hardness
(
η) are shown in Table 5. The diꢀerent thiosemicabazone
ligands are optimized in the thiol structure as mentioned
in the previous characterization part. The stability of the
coumarin thiosemicarbazone nucleus increases by the excess
fused benzene ring or bromo derivative, due to the resonance
increase as indicated by the results of the ligands’ energies.
The three Pd (II) complexes have comparable reactivity due
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Chemical Papers
Fig. 8 The cell viability
(
HCT116 human colon cancer)
with the concentration change
of the suggested drugs of Pd(II)
complexes
bond angles of the ligands are changed relatively upon coor-
dination to optimize the values of the square planar geom-
etry angles as mentioned in Table 6.
that Pd (II) ion was bonded to the ligands via N, O and
S donor atoms. The HOMO and LUMO molecular orbital
energy diagrams are presented in Fig. 4.
Table 7 presents the atomic charge distribution of the
ligands and their Pd (II) complexes by (MPA) and (NPA).
The decrease or increase in the bond length between atoms
depends on the positively and negatively charge distribu-
tion. NBO analysis shows that O16, N22 and N25 atoms in
the ligands have the most negative atomic charges. Upon
chelation, the charges of the carbonyl oxygen (O16) and sul-
fur (S28) atoms have an eꢀective decrease in their electron
density values, accompanied by a decrease in the remaining
neighboring atoms due to their participation in the coordina-
tion to the Pd(II) ion caused by (L→M) ligand to palladium
charge transfer. The charge of the nitrogen (N22) atom has a
slight increase in its negative value due to the electron back-
donation from the palladium ion to the donating nitrogen site
Microbiological and docking investigations
The disc diꢀusion assay was used to determine if the tested
ligands and their pd(II) complexes could inhibit the growth
of bacteria, by testing the previously investigated compounds
against different types of bacteria that consist of two of
each Gram-positive and Gram-negative types. OCETh and
BOCETh ligands and their pd(II) complexes have higher anti-
bacterial eꢀects than NOCETh ligand and its pd(II) complex
as seen in the inhibition zone values described in Table 8 and
Fig. 5. This may be due to the increase of liposolubility of the
tested compounds, which is a favored property to enhance the
passage of the suggested drugs through the lipid layers of the
microorganisms (Carcelli et al. 1995; Yoon et al. 2013) and,
consequently, devastating them more aggressively. OCETh
and BOCETh ligands and their Pd(II) complexes have lower
dipole moment values than their corresponding values in the
case of the NOCETh ligand and its Pd(II) complex, which
means that the less polar drug assists in the penetration of the
cell wall and then shifting to the more toxic drug within the
cellular environment (Carcelli et al. 1995; Yoon et al. 2013).
Molecular docking investigation was conducted for the evalu-
ation of the possible mode of action between the examined
compounds and the receptor. Hydrogen bonds play an impor-
tant role in the antibacterial activity through their formation
(
Hassan 2017). The electron density on the Pd (+2) atom
center increases after complexation, because (L → M) the
donor atom’s charge transfer of the investigated ligands to
the central Pd ion. So, the theoretical investigation supported
between the important terminal amino (–NH ) group with the
2
active center of cell constituents, thereby causing considerable
interference with normal cell process as expected from the
docking results Fig. 6. The amino acids involved in the active
pocket in 3Å with their bond lengths are tabulated in Table 9.
Fig. 9 IC50 values of the suggested drugs of Pd(II) complexes
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Chemical Papers
Fig. 10 The docked results of Pd–OCETh, Pd–BOCETh and Pd–NOCETh to the receptor tyrosine kinase (colon anticancer activity) (PDB ID:
2
J5F), respectively
NOCETh shows the presence of arene–arene interaction with
Trp-74. A DMF molecule in pd(II) complexes has a great
interaction eꢀect by showing hydrogen bond formation. Ring
arene–cation interaction with Arg- 26 is observed through the
docking of Pd–OCETh and the metal contact receptor with
cys-1 through pd–BOCETh as observed in Fig. 7. Docking
investigation conꢁrms the output experimental results for
OCET, BOCET, NOCET and their Pd (II) complexes. For the
interaction of the synthesized compounds with the selected
receptor, OCET, BOCET and their Pd(II) complexes show
more negative binding energy values than NOCET ligand and
its Pd(II) complex as shown in Table 9. The more negative
binding energy values mean a more spontaneous and favored
interaction.
Antitumor activity and docking investigations
Cytotoxicity against a human colon carcinoma cell line
(HCT116)
The selected Pd(II) complexes were tested for their cytotoxic-
ity against HCT116 human colon cancer cell lines to judge
their utility for further development as anticancer agents. The
experimental study of the cell viability with the concentration
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Chemical Papers
change is shown in Fig. 8. The results clearly show a con-
centration-dependent inhibition of cancer cell by the three
complexes. The concentration required to reduce the growth
of cancer cells by 50% (IC50) for all complexes was observed
in (Fig. 9). All complexes exhibited highly cytotoxicity in
the order Pd–BOCETh>Pd–OCETh>>Pd–NOCETh. The
stronger activity of OCETh and BOCETh palladium com-
plexes could possibly be attributed to a higher cellular uptake
due to an increased lipophilicity as observed from their values
of dipole moments. Docking study was performed to evaluate
the binding aꢂnity of the inhibitors within the protein mol-
ecules. The docking study was performed using the known
human colon cancer target protein CDK2 (PDB ID: 2R3 J)
transition series metal ions. X-ray crystal structure of a dinu-
clear copper(II) complex. J Inorg Biochem 57:43 PMID:
7
876834
Chmara H, Borowski E (1986) Bacteriolytic eꢀect of cessation
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Cutillas N, Yellol GS, de Haro C, Vicente C, Rodríguez V, Ruiz J
(
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Deming DA, Maher ME, Leystra AA, Grudzinski JP, Clipson L,
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Downing RS, Urbach FL (1969) Circular dichroism of square-planar,
tetradentate Schiꢀ base chelates of copper (II). J Am Chem Soc
(
Yoon et al. 2013). Docking results for colon cancer target
9
1:5977. https://doi.org/10.1021/ja01050a009
CDK2 of Pd–OCETh, Pd–BOCETh and Pd–NOCETh show
signiꢁcant binding aꢂnity as seen in Fig. 10. Pd–OCETh,
Pd–BOCETh and Pd–NOCETh show hydrogen bonds with
El-Gammal OA (2010) Synthesis, characterization, molecular
modeling and antimicrobial activity of 2-(2-(ethylcarba-
mothioyl)hydrazinyl)-2-oxo-N-phenylacetamide copper com-
plexes. Spectrochim Acta A 75:533. https://doi.org/10.1016/j.
saa.2009.11.007
(
Ly-129 and Gln-131), (Lys-20 and Lys-89) and (Lys-129),
respectively. The binding energies (kcal/mol) and the RMSD
Emeléus HJ, Sharpe AG (1981) Advances in inorganic chemistry and
radiochemistry. Academic Press, London.
(
Å) values for Pd–OCETh, Pd–BOCETh and Pd–NOCETh
are (− 10.21 & 1.20), (− 10.29 & 1.26) and (− 10.06 & 0.79),
respectively.
Fessenden RJ, Fessenden JS (1990) Inorganic chemistry. Cole Pub-
lishing Company, Belmont, p 587
Gomha SM, Khalil KD (2012) A Convenient ultrasound-promoted
synthesis and cytotoxic activity of some new thiazole deriva-
tives bearing a coumarin nucleus. Molecules 17:9335–9347
Gomha SM, Zaki YH, Abdelhamid AO (2015) Utility of 3-acetyl-6-
bromo-2H-chromen-2-one for synthesis of new heterocycles as
potential antiproliferative agents. Molecules 20:21826–21839
Hassan SS (2017) DFT and molecular docking studies of Rh(III)
complexes of Coumarinyl–Thiosemicarbazone nuclei based
ligands. Appl Organomet Chem 32:1. https://doi.org/10.1002/
aoc.4170
Conclusions
Pd(II) complexes of coumarinyl thiosemicarbazone deriva-
tive ligands were characterized by physicochemical tools. It
was found that the ligands act as a uninegatively tridentate
ligands, attached to the Pd(II) ions as 1:1 complexes via
azomethine (N), carbonyl oxygen and deprotonated thiol
Hassan SS, Shoukry MM, Shallan RN, van Eldik R (2017) Synthe-
sis, characterization, speciation and biological studies on metal
chelates of 1-benzoyl(1,2,4-triazol-3-yl)thiourea. J Coord Chem
70:1761. https://doi.org/10.1080/00958972.2017.1312357
Huang W, Liu G, Zhang X, Fu W, Zheng S, Wu Q, Liu C, Liu Y,
Cai S, Huang Y (2014) Cost-eꢀectiveness of colorectal cancer
screening protocols in urban chinese populations. PLoS ONE.
https://doi.org/10.1371/journal.pone.0109150
(
S) with the formation of square planar structures. DFT
calculation was carried out for the prepared three ligands
and their Pd(II) complexes with the calculation of charge
distribution within the ligands and their Pd(II) complexes
using Mulliken population analysis (MPA) and natural popu-
lation analysis (NPA). The stronger antibacterial activity of
OCETh and BOCETh ligands and the antitumor activity of
their palladium (II) complexes could possibly be attributed
to a higher cellular uptake due to an increased lipophilic-
ity as observed from their values of dipole moments. The
docking stimulation pointed out the binding model of the
studied compounds by using the protein GlcN-O-P synthase
Kapdi AR, Fairlamb IJ (2014) Anti-cancer palladium complexes: a
focus on PdX2L2, palladacycles and related complexes. Chem
Soc Rev 43(13):4751–4777
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7
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ja01023a012
(
antimicrobial activity)(PDB ID: 1XFF) and EGFR tyrosine
kinase (anticancer activity) (PDB ID: 2R3 J).
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