Biological interaction between copper(II) complex and nucleosides

Article abstract of DOI:10.14233/ajchem.2014.16964

A copper-coordinated complex based on 7-membered amide cycle has been designed and synthesized. Its binding properties for various nucleosides, guanosine-5'-diphosphate (GDP), uridine-5'-diphosphate (UDP), inosine-5'- diphosphate (IDP) and guanosine-5'-tr

Full text of DOI:10.14233/ajchem.2014.16964

Asian Journal of Chemistry; Vol. 26, No. 14 (2014), 4457-4461
ASIAN JOURNAL OF CHEMISTRY
http://dx.doi.org/10.14233/ajchem.2014.16964
Biological Interaction Between Copper(II) Complex and Nucleosides
1
1
2
1
3,*
YAPING GUO , XIUJU WANG , LEIMING LUO , JINGE DU and XUEFANG SHANG
1
2
3
Department of Chemistry, Sanquan College of Xinxiang Medical University, Jinsui Road 601, Xinxiang 453003, Henan Province, P.R. China
Department of Pharmacy, Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, Henan Province, P.R. China
Department of Chemistry, Xinxiang Medical University, Jinsui Road 601, Xinxiang 453003, Henan Province, P.R. China
*
Corresponding author: Fax +86 373 3029959; Tel +86 373 3029128; E-mail: xuefangshang@126.com; gypapply@163.com
Received: 30 December 2013; Accepted: 23 March 2014; Published online: 5 July 2014;
AJC-15496
A copper-coordinated complex based on 7-membered amide cycle has been designed and synthesized. Its binding properties for various
nucleosides, guanosine-5'-diphosphate (GDP), uridine-5'-diphosphate (UDP), inosine-5'- diphosphate (IDP) and guanosine-5'-triphosphate
(
GTP) has been studied by UV-visible spectra and crystal structure. Results indicated that the compound showed the highest binding
ability with guanosine-5'-triphosphate in water solution among the studied nucleosides. The interaction of host-guest derived from hydrogen
bonding and π-π staking and the host-guest binding ability depended on the chain length of nucleosides. In addition, the compound can
be used to label nucleoside.
Keywords: Biological interaction, Nucleoside, Copper(II) complex.
inosine-5'- diphosphate (IDP) and guanosine-5'-triphosphate
INTRODUCTION
(
GTP) which selectively complexes with GTP in neutral water
In recent years, increasing attention in the field of host-
guest chemistry has been devoted to the fast development of
solution and signals the event through changes in absorption
spectroscopy.
1-7
anion recognition systems . Detection of nucleosides has para-
mount importance as they form the fundamental units of all
EXPERIMENTAL
8
-12
the life forms . Most known molecular receptors for the
nucleosides use complementary hydrogen bonding, but such
recognition in the aqueous medium would be limited due to
the interference from hydroxyl groups of the sugar moiety
Most of the starting materials were obtained commercially
and all reagents and solvents employed were of analytical grade.
All nucleosides (GDP, UDP, IDP and GTP) were purchased
from Sigma-Aldrich Chemical Co., stored in a desiccator under
vacuum containing self-indicating silica and used without any
further purification. Dimethyl sulfoxide (DMSO) was distilled
1
3-15
and competitive hydrogen bonding of the solvent . More-
over, the sugar moiety of the nucleosides can interfere in such
recognition and hence masking of the hydroxyl groups prior
in vacuo after dried with CaH . C, H, N elemental analysis was
2
16
1
to the recognition event is essential . In previous reported lite-
rature, the recognition of nucleosides was focused on supra-
made onVanio-EL. H NMR spectrum was recorded on aVarian
UNITY Plus-400 MHz Spectrometer. FAB-MS was made on
VG ZAB-HS. ESI-MS was performed with a MARINER
apparatus. UV-visible Spectroscopy titrations were made on a
Shimadzu UV2550 Spectrophotometer at 298 K. The stability
17,18
molecular catalysis area at certain pH condition . In addition,
the literature about the recognition of ATP has been reported
due to the important role that ATP transports chemical energy
1
6,19-21
within cells for metabolism
. Nowadays, the methods
constants K were obtained by the non-linear least square
s
detecting nucleotides are usually liquid chromatography (LC),
high performance liquid chromatography (HPLC) and electro-
spray ionization mass spectrometry (ESI-MS) . However,
studies on detecting nucleotide with new compounds are less
reported.
According to the above information, we synthesized a
new compound 1 (Scheme-I) and fortunately obtained its
crystal. The nucleotide binding ability of compound 1 with
guanosine-5'-triphosphate (GDP), uridine-5'-diphosphate (UDP),
calculation method through data fitting.
Compound 1 was synthesized according to the route
shown in Scheme-II.
Benzo-1,4-diazacycloheptane[2,3-d]-5,7-dione (2) :
1,2-Phenylenediamine (10.8 g, 0.1 mol), diethyl malonate (16
mL, 0.1 mol) and pyridine (200 mL) were put in a 250 mL
2
2-24
2
5
three-neck flask. The mixture was refluxed with N for 72 h.
2
After cooling, the mixture was filtrated and the colourless solid
obtained. The solid was washed with ethanol and ether

4
458 Guo et al.
Asian J. Chem.
H
N
O
N
H
O
N
Br
N
O
N
N
Br
NH
O
O
O
Cu
O
NH2
-
O P O P O
O-
Br
O
n
O-
H
H
H
N
N
O
Br
H
H
OH
OH
N
H
n=1, GDP; n=2, GTP
O
1
O
OH
N
N
N
HN
O
O
O
O
O
-O P O P O
O- O-
-O P O P O
N
N
H
O
O
H
H
O-
O-
H
H
H
H
OH
H
OH
OH
OH
IDP
UDP
Scheme-I: Chemical structures of compound 1 and nucleosides
H
N
O
O
H
N
O
O
NH2
O N
2
CH (COOC H )
5 2
fuming HNO3
2
2
pyridine, reflux
NH2
N
H
N
H
3
2
Br
Br
OH
OH
H
O
O
H N
2
N
Pd/C H2
Br
CHO
Br
H
N
O
O
N
N
H
N
H
4
5
Cu(NO3)2
DMF
1
Scheme-II: Synthesis route for compound 1
1
sequentially and dried in vacuum.Yield: 72 %. H NMR (400
with distilled water, recrystallized from methanol and dried in
1
MHz, DMSO-d
6
, 298 K) δ 10.38 (s, 2H), 7.11-7.18 (m, 4H),
: C, 61.36;
vacuum. Yield: 85 %. H NMR(400 MHz, DMSO-d
δ 10.96 (s, 1H), 10.74 (s, 1H), 8.04, 7.3 (3H), 3.3 (s, 2H),
Elemental analysis: Calc. for C : C, 48.88; H, 3.19; N,
6
, 298 K)
3
.17 (s, 2H). Elemental analysis: Calc. for C
H
9 8
N
2
O
2
H, 4.58; N, 15.90; Found: C, 61.69; H 4.59; N, 15.96. FAB-
H N O
9 7 3 4
+
MS (m/z): 177.0 (M + H) .
19.00; Found: C, 48.76; H 3.58; N, 18.61. ESI-MS (m/z): 220.9
–
(
4'-Nitrobenzo)[1', 2'-d]-1,4-diazacycloheptane[2,3-d]-
,7-dione (3): Benzo-1,4- diazacycloheptane[2,3-d]-5,7-dione
10 mmol, 1.7 g) was dissolved in concentrated H SO (43
(1.1 mL) was added dropwise with stirring
at 273 K. After the addition was completed, the mixture was
stirred for 2 h and then poured into 200 mL ice-water. The
solution was filtered to give a yellow solid, which was washed
(M-H) .
5
(4'-Aminobenzo)[1',2'-d]-1,4-diazacycloheptane[2,3-
d]-5,7-dione (4): A slurry of compound (4'-nitrobenzo)[1',2'-
d]-1,4-diazacycloheptane[2,3-d]-5,7- dione (221 mg) and Pd/C
(10 %, 70 mg) in dry ethanol (200 mL) was maintained under
hydrogen with stirring for 12 h. The mixture was filtered through
a bed of Celite and then washed twice with ethanol (2 × 20 mL).
(
2
4
mL). Fuming HNO
3

Vol. 26, No. 14 (2014)
Biological Interaction Between Copper(II) Complex and Nucleosides 4459
The solvents were removed under reduced pressure and the
yellowish solid dried in vacuum. Yield: 92 %. H NMR (400
was uncoordinated DMF (O5) (Table-1). The overall crystal
structure featured chain type with DMF molecules by hydrogen
1
MHz, DMSO-d
H), 6.38 (m, 1H), 6.27 (d, 2H), 5.16 (s, 2H) 3.08 (s, 2H).
Elemental analysis: Calc. for C : C, 56.54; H, 4.74; N,
1.98; Found: C, 56.41; H 4.96; N, 21.87. ESI-MS (m/z): 190.3
6
, 298 K) δ 10.15 (s, 1H), 9.91 (s, 1H), 6.76 (d,
bonds along the b axis.
1
H N O
9 9 3 2
Br2A
C4A
2
C5A
C3A
C2A
–
(
M-H) .
N-(2"-Hydroxyl-3",5"-dibromophenyl-methylene-yl)-
'-imino-benzo[1',2'-d]-1,4-diazacycloheptane[2,3-d]-5,7-
dione [HODBrphC=NphDNHexDO](5): (4'-amino-benzo)-
1',2'-d]-1,4-diazacycloheptane[2,3-d]-5,7-dione (1 mmol, 191
Br1A
C1A
02A
C12
N3
C6A
N2A
C7A
C9A
03
0
1A
4
C15A
C13
C8
C14A
C16A
C11
C10
C16
N1A
C8A
C10A
Cu1
C14
C15
[
C13A
N1
C11A
C12A
01
C9
N2
mg) and 3,5-dibromo-salicylaldehyde (1 mmol, 278 mg) were
suspended in dry ethanol (100 mL). The mixture was heated
under reflux for 8 h and the orange-yellow precipitate was
separated by filtration. The solid was washed with diethyl ether
03A N3A
C7
02
C1
C6
C5
Br1
C2
C3
C4
1
and dried under vacuum. Yield: 89 %. H NMR (400 MHz,
Br2
DMSO-d
.9 (d, 2H), 7.3 (d, 2H), 7.2 (m, 1H) 3.24 (s, 2H). Elemental
analysis: Calc. for C16 Br : C, 42.41; H, 2.45; N, 9.27;
Found: C, 42.35; H 2.88; N, 9.45. ESI-MS (m/z): 449.8
6
, 298 K) δ 14.41 (s, 1H), 10.54 (s, 2H), 8.97 (s, 1H),
Fig. 1. Crystal structure of 1 and the hydrogen atoms are shown as small
circles with arbitrary radii (ellipsoids at 50 % probability)
7
H
11
N
3
O
3
2
The nucleotide binding ability of 1 with GDP, UDP, IDP
and GTP were investigated through UV-visible spectral titra-
–
(
M-H) .
Cu(II)[HODBrphC=NphDNHexDO]2 (1): 5 (0.1
mmol) and Cu(NO (0.05 mmol) were stirred for 1 h in DMF
20 mL), then stood at room temperature. After 24 h, the green
expected compound appeared. Elemental analysis: Calc. for
Br Cu·5H O: C, 39.72; H, 2.08; N, 8.68; Found:
tions in DMSO/H O (90:10) by the addition of GDP, UDP, IDP
2
and GTP to the solution of 1. The interacted absorption spectra
of compound 1 with nucleosides was shown in Fig. 2. With
the addition of GDP, the absorbance band at about 323 nm
decreased gradually and a new absorbance band developed at
about 425 nm. In addition, one clear isosbestic point appeared
at about 373 nm, which showed a stable concentration of the
complex was formed in the solution with a certain stoichio-
metric ratio between 1 and GDP. The addition of UDP, IDP
and GTP also induced similar spectral changes of compound
)
3 2
(
C
32
H N O
20 6 6
4
2
C, 39.22; H 3.55; N, 8.91.
X-Ray crystallography:A green crystal of 1 with dimen-
sions of 0.20 × 0.14 × 0.06 mm was mounted on a glass fiber.
X-ray single-crystal diffraction data were collected on a Rigaku
Saturn CCD area detector at 294(2) K with MoK
α
radiation (λ
1
, compared with GDP. Differently, the concentration of
=
0.71073 Å) . The structure was solved by direct methods
2
nucleosides was different when the equilibrium developed.
The above results showed compound 1 interacted with GDP,
UDP, IDP and GTP. Job-plot of compound 1 with GDP showed
compound 1 bound GDP at 1:1.
and refined on F by full-matrix least squares methods with
26
SHELXL-97 .
RESULTS AND DISCUSSION
Compound 1 was obtained by the reaction of 5 and
Cu(NO in N,N-dimethylformamide (DMF). The crystals of
Stability constants of compound 1 for nucleosides were
calculated according to the equation (1), 1:1 host-guest
)
3 2
2
7-30
compound 1 suitable for X-ray crystal analysis has been obtained
and the structure has been confirmed (Fig. 1). The overall coor-
dination environment of the Cu(II) atom involved two compound
complexation
.
2
X = X + 0.5∆ε{c
0
H
+ c
G
+ 1/K
s
-[(c
-4c
are the concentration of guest and host,
respectively. X is the intensity of absorbance at certain concen-
tration of host and guest. X is the intensity of absorbance of
host when the anion isn't added. K is the affinity constant of
H
+ c
G
+ 1/K
] }
s
)
1
/2
H
c
G
(1)
1
and two DMF molecules. Four of the Cu1-O1, Cu1-O1A,
Cu1-N1, Cu1-N1A bonds were relatively longer (bond lengths
.913 Å, 1.914 Å, 2.033 Å and 2.033 Å) and they constituted
a plane quadrangular geometry around the Cu(II) atom
O1-Cu1-O1A, 180°, O1-Cu1-N1, 90.7°, O1-Cu1-N1A, 89.3°,
O1A-Cu1-N1, 89.3°, O1A-Cu1-N1A, 90.7°, N1-Cu1-N1A,
80°); the other two Cu-O4, Cu-O4A contacts were
where c
G
and c
H
1
0
s
(
host-guest complexation. ∆ε is the change in molar extinction
coefficient.
Curve fitting (about 425 nm) of the interaction between
the compound and GDP, UDP, IDP, GTP according to equation
(1) was shown in Fig. 3. The high correlation also indicated
compound 1 bound nucleosides at 1:1.
1
significantly shorter (bond lengths 1.653 Å and 1.653 Å),
completing a distorted octahedron as the overall geometry
around the Cu(II) atom. The NH of amide formed hydrogen
bonds with oxygen atoms of DMF molecules that were derived
from two resources: one was coordinated DMF (O4), the other
According to UV-visible titration data, the stability constants
of compound 1 with various nucleosides were determined by
TABLE-1
INTERMOLECULAR HYDROGEN BONDS IN COMPOUND 1
Donor---H… Acceptor
N2---H2 … O5
N3A---H3A … O4
[ARU]
x, 1+y, z
x, -1+y, z
D-H (Å)
0.872
0.943
H…A(Å)
1.991
0.943
D…A(Å)
2.855
2.890
D-H … A(°)
170.10
166.98

4
460 Guo et al.
Asian J. Chem.
1
0
0
0
.00
.75
.50
.25
0
1.00
(
a)
(b)
0.75
0.50
0.25
0
3
00
350
400
450
500
550
3
00
350
400
450
500
550
Wavelength (nm)
Wavelength (nm)
1
.00
1
0
0
0
.00
.75
.50
.25
0
(
c)
(d)
0.75
0.50
0.25
0
3
00
350
400
450
500
550
300
350
400 450
Wavelength (nm)
500
550
Wavelength (nm)
-5
-1
Fig. 2. UV-visible spectral changes of compound 1 (2 × 10 mol L ) upon the addition of GDP(a), UDP(b), IDP(c), GTP(d), the concentration of nucleosides
-5
-1
is from 0 to 160 × 10 mol L . Arrows indicate the direction of increasing nucleosides concentration
0.40
0.35
0.30
0.25
0.20
0.15
0.10
0.40
0.35
0.30
0.25
(a)
(b)
0.20
0.15
0.10
–2
0
2
4
6
8
10 12 14 16 18
–2
0
2
4
6
8
10 12 14 16 18
–1
–4
–4
× 10 mol L
–1
C
G
× 10 mol L
C
G
0.40
0.35
0.30
0.25
0.20
0.15
0.10
(c)
(d)
0
0
0
0
0
0
0
.35
.30
.25
.20
.15
.10
.05
–2
0
2
4
6
8
10 12 14 16 18
–1
–2
0
2
4
6
8
–4
10 12 14 16 18
–1
–
4
C
G
× 10 mol L
C
G
× 10 mol L
Fig. 3. Curve fitting (about 425 nm) of the interaction between the compound 1 and GDP(a), UDP(b), IDP(c), GTP(d)

Vol. 26, No. 14 (2014)
Biological Interaction Between Copper(II) Complex and Nucleosides 4461
non-linear least square method and listed in Table-2. Obviously,
the binding ability of nucleosides with compound 1 was in the
order: GTP > GDP-IDP-UDP (in the range of error). The binding
ability of GTP with compound 1 was the strongest among the
studied nucleosides.As for the same length of phosphate chain,
the value of stability constant between GDP, UDP, IDP and
compound 1 was almost equal in the range of error.According
to the crystal structure of compound 1, nucleosides may interact
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1
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-
1
Nucleosides
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K (mol L)
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