JBIC Journal of Biological Inorganic Chemistry

, Volume 22, Issue 7, pp 1055–1064 | Cite as

Anticancer activity of novel amino acid derivative of palladium complex with phendione ligand against of human colon cancer cell line

Original Paper

Abstract

The aim of this work is the identification of the structural effect of amino acid–Pd complex on DNA as an intracellular target which was studied using various spectroscopic techniques such as fluorescence, UV–visible and circular dichroism in combination with a molecular docking study. Hence, a novel water-soluble palladium complex, [Pd(phendione)(isopentylglycine)]NO3, has been synthesized and characterized by spectroscopic method. The anticancer activity of complex was investigated against human colon cancer cell line of HCT116 after 24 h of incubation using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. In addition, this complex was interacted with calf thymus DNA (ct-DNA) via positive cooperative interaction. The fluorescence data indicate that Pd complex is intercalated in DNA. These results were confirmed by circular dichroism spectra. The molecular docking results indicate that docking may be an appropriate method for the prediction and confirmation of experimental results. Complementary molecular docking results may be useful for the determination of the binding mechanism of DNA in pharmaceutical and biophysical studies providing new insight into the novel pharmacology and new solutions in the formulation of advanced oral drug delivery systems.

Graphical Abstract

Docking and spectroscopic studies show that new water-soluble Pd complex has anticancer activity and it can bind to DNA via intercalation and groove binding.

Keywords

Anticancer palladium complex Human colon cancer Phendione DNA binding Amino acid derivative Molecular docking 

Introduction

Transition metal ions play an important role in the body’s biological activity [1, 2]. Medicinal properties of transition metals in coordination with ligands is different. In pharmaceutical compounds, silver is antimicrobial, gold is antiarthritic, bismuth is antiulcer, antimony is antiprotozoal, vanadium is antidiabetic, iron is antimalarial and platinum is anticancerous in chemotherapy [3]. Focused on side effects of anticancer platinum drugs, especially cisplatin, necessary research continues to formulate new complexes with fewer side effects [4].

Using bidentate ligands such as amino acid derivatives is the strategy in designing new drugs [5]. Due to the presence of lipophilic functional groups, toxicity of drug is reduced and influence of the drug into the cancer cells is improved [6]. In addition, due to structural similarity, palladium complex is the best candidate for anticancer platinum drugs [7]. For reactivity, kinetically and lipolicity control of palladium complexes, chelating of Pd with aromatic N- and N, N- donor ligand such as Phendione and phenanthroline derivatives can be used [8, 9, 10, 11].

According to the reports, metal complexes with phenanthroline derivatives have shown anticancerous [12, 13, 14, 15, 16, 17, 18, 19], antiviral [20, 21, 22], anti-bacterial [23, 24, 25, 26] and antifungal effects [27, 28, 29].

Among these compounds, 1,10-phenanthroline-5,6-dione, phendione, is a chelated ligand with many biological properties [30].

Accordingly, phendione plays an important role in anticancer activities with and without metals [31, 32, 33] and shows different biological activities in the presence of various metals [17, 34].

In addition, the interaction mode of Pd complex with DNA depends on ligand environment and complex structure, as intracellular target. Hence, in this study, a new anticancer candidate of Pd complex with amino acid and phendione ligands (Scheme 1) has been synthesized and characterized. The mechanism of the interaction of DNA with mentioned Pd complex was determined and binding parameters were measured. Complementary molecular docking results may be useful for the determination of the binding mechanism of DNA in pharmaceutical and biophysical studies providing new insights into the novel pharmacology and new solutions in the formulation of advanced oral drug delivery systems.
Scheme 1

Proposed structure of Pd complex

Experimental

Materials and methods

The chemicals and the solvents were purchased by Merck and used as received. Calf thymus DNA, sodium salt and Tris–HCl buffer were purchased from Sigma–Aldrich. Palladium(II) chloride was obtained from Fluka. 1,10-Phenanthroline-5,6-dione (phendione) [35, 36], isopentyl glycine [37] and [Pd(phendione)Cl2] [38] were prepared according to the literature methods. Infrared spectra (4000–400 cm−1) were determined in KBr disks on a JASCO-460 plus FT-IR spectrophotometer. UV/VIS spectra were recorded on a Spekol 2000 UV/VIS recording spectrophotometer. 1H NMR spectra were measured on a Brucker DRX-300 Advance spectrometer at 300 MHz, using TMS as the internal reference in DMSO-d6. The fluorescence spectra were carried out on a JASCO 6200 spectrofluorometer. Double-distilled water was used as solvent. Carbon, hydrogen and nitrogen in the ligand and the complex were analyzed on a Herause CHN-RAPID elemental analyzer. Circular dichroism (CD) measurements were carried out with a JASCO FP-6500 spectrophotometer.

Synthesis of [Pd(phendione)(isopentylglycine)]NO3

This complex was synthesized by converting [Pd(phendione)Cl2] complex into a diaqua complex by silver nitrate method: 0.387 g of [Pd(phendione)Cl2] (1 mmol) was suspended in 90 mL of double-distilled water/acetone (3/1, v/v). To this suspension, 0.339 g of AgNO3 (2 mmol) in 20 mL of water was added slowly with continuous stirring. The reaction mixture was heated with stirring at 50 °C for 2 h and at the room temperature for 16 h under dark. Then, the mixture was filtered to remove AgCl. This filtrate was mixed with 0.182 g of (3-methylbutyl) glycine hydrochloride (1 mmol) and 0.168 g of NaHCO3 (2 mmol) dissolved in 9 mL of distilled water. The reaction mixture was further stirred at 45 °C for 2 h. Then light brown-green solution was filtered and concentrated at 35 °C to 15 mL. The trace amount of turbidity formed was filtered and the clear brown-green filtrate was further concentrated to about 5 mL at 35 °C. The brown-green crystals formed were filtered and washed with small amount of chilled double-distilled water and then dried in a vacuum oven at 35 °C. Synthesis of ligands and complex are shown in Scheme 2. Yield: 50%, analytical calculated for C19H20N4O7Pd (522.81): C, 43.65, H, 3.86, N, 10.72%. Analytical found: C, 43.7, H, 3.76, N, 10.78%, 1H NMR (300 MHz, DMSO-d6): 0.91 (t, 6H), 1.39 (m, 2H), 1.59 (m, 1H), 2.53 (t, j = 26.5 Hz, 2H), 3.49 (s, 2H), 7.21 (m, 2H), 7.85 (s, NH), 7.94 (d, j = 6.7 Hz 2H), 8.79 (d, j = 3.5 Hz, 2H), IR (cm−1, KB, disk): 1360(s, C=N), 1617(s, C=O), 1739(s, O–C=O), 2855(s, C–H), 2920(s, =C–H), 3419(s, NH), UV band maxima in nm (Ɛm in L mol−1 cm−1×10−4): 224(0.12), 270(0.05), molar conductance of 0.1 mM: 120.3 cm2 ohm−1 mol−1.
Scheme 2

General preparation route for the ligand and Pd complex

Biochemical studies

Tris–HCl buffer, pH 7.4, containing 10 mmol L−1 sodium chloride was used for all experiments. The stock solution of DNA (4 mg/mL) was prepared by continuous stirring at 4 °C until homogenous solution was achieved. The DNA concentration was measured by Beer–Lambert law at 258 nm (ε = 6.6 cm−1 L (103 nucleotide)−1 [39]. The stock solution of Pd(II) complex (1 mmol L−1) was made with stirring at 35 °C. The incubation time was 1 h for the solution of DNA–Pd complex at 27 and 37 °C. The incubation time is the time required for completing DNA–complex interaction and with no change in absorbance.

Denaturation of DNA with Pd complex

When the Pd complex binds to DNA, unfolding of DNA occurs. Due to denaturation, the absorption at 258 nm is changed. In this experiment, the reference cell was filled with 1.8 mL of Tris–HCl buffer and the sample cell was filled with 1.8 mL of Tris–HCl buffer containing 80 mmol L−1 DNA where absorption of these solutions are ~0.5–0.6 at constant temperatures of 27 or 37 °C. Then, 25 µL of Pd(II) complex (1 mmol L−1 stock solution) was added to each cell in each injection. The injection was continued and the absorption was recorded at 258 nm for DNA and at 640 nm to eliminate the interference of turbidity after 3 min until the absorption reading does not change. Here, transition curve, for native to denatured state of DNA, was obtained. From these curves, the concentrations of Pd (II) complex at the midpoint of transition ([L]1/2) were determined at both temperatures.

In addition, the binding and thermodynamic parameters and the types of binding between this complex and DNA are mainly determined using the followed method: These include the conformation stability of DNA in the absence of metal complexes (\(G^{^\circ } = G^{^\circ }_{{{\text{H}}_{ 2} {\text{O}}}} - m\left[ {\text{complex}} \right]\), where m is the ability of DNA denaturation by complex, G° = −RTlnK, K = [ANAobs]/[Aobs − AD], Aobs is the observed absorbance used to follow unfolding in the transition region, AN and AD are the values of absorbance to the native and denatured conformations of DNA; the heat needed for DNA denaturation in the absence of metal complexes, \((H^{^\circ } = \left( {G^{^\circ }_{(T1)} /T_{1} - G^{^\circ }_{T2} /T_{2} } \right)\)/(1/T1 − 1/T2); and the entropy of DNA unfolding by Pd(II) complex, \(S^{^\circ }_{{\left( {{\text{H}}_{ 2} {\text{O}}} \right)}} \left( {\Delta G^{^\circ }_{{\left( {{\text{H}}_{ 2} {\text{O}}} \right)}} = \Delta H^{^\circ }_{{\left( {{\text{H}}_{ 2} {\text{O}}} \right)}} - T - S^{^\circ }_{{\left( {{\text{H}}_{ 2} {\text{O}}} \right)}} } \right)\).

Thermal denaturation studies

Thermal stability of free DNA and DNA–Pd complex were investigated by monitoring absorbance intensities at different temperatures. The scan rate was 2 °C/min at 258 nm for solutions of DNA (50 µM) in the absence and presence of the complex at a fixed concentration (r = [complex]/[DNA] = 1.06). The absorption data were plotted as a function of temperature. The melting temperature Tm, which is defined as temperature where half of the total base pair is unbounded, was determined as transition midpoint of the melting curve.

Fluorescence studies

The maximum quantum yield for ethidium bromide (EB) was achieved at 471 nm, so this wavelength was selected as the excitation radiation for all samples at 27 °C and in the emission range of 540–700 nm. The widths of the excitation and the emission slit were set at 5.0 nm. At first, 60 µmol/L DNA was added to 2 µmol/L aqueous EB. The effect of complex on the fluorescence intensity of DNA–EB was studied. Thus, the titration of DNA–EB with complex, covering a range of [com]/[DNA] ratio in the transition region, formed from the denaturation experiment of DNA with Pd complex was performed by increasing the concentration of complex (0.3, 0.6 to 1.8 mmol/L). It is important that this Pd complex does not exhibit emission in the presence of DNA and does not influence the emission intensity of free EB in the absence of DNA.

Circular dichroism (CD) measurements

The CD measurements of the interaction between metal complex and DNA are useful in monitoring the changing DNA conformation. When DNA is titrated by Pd complex, CD spectra display changes for both positive band at 265 nm, which is related to base stacking, and negative band at 247 nm, which is related to helicity. CD data were recorded, while the concentration of DNA was kept constant (120 μmol L−1) and the Pd(II) complex concentrations (0.13, 0.23 and 0.33 mmol L−1) were changed. Each sample was scanned at a wavelength range between 200 and 320 nm [40].

Cytotoxic studies

Cell culture

HCT116 cells were obtained from the National Cell Bank of Iran (NCBI), Pasteur Institute of Iran. The cells were grown on the DMEM medium (Sigma) supplemented with l-glutamine (2 mM), streptomycin, penicillin (5 µg/ml), and 10% heat-inactivated fetal calf serum at 37 °C under a 5% CO2/95% air atmosphere.

Cell proliferation assay

The new designed Pd(II) complex synthesized inhibits the growth of human colon cancer cell line HCT116. The growth inhibitory activity of the complexes was measured by MTT assay. The cleavage and conversion of the soluble yellowish MTT to the insoluble purple formazan by active mitochondrial dehydrogenase of living cells has been used to develop an assay system alternative to other assays for measurement of cell proliferation. The harvested cells were seeded into a 96-well plate (1 × 104 cell/ml) and were left to adhere overnight. Prior to the experiments, the cells were twice washed with phosphate-buffered saline (PBS). Then, the cancer cells were incubated with different concentrations of sterilized Pd(II) complex (0–350 µM) and incubated for 24 h. Four hours to the end of the incubation, 25 µL of the MTT solution (5 mg/ml in PBS) was added to each well containing fresh and cultured media. At the end, the insoluble formazan produced was dissolved in a solution containing 10% SDS and 50% DMF (left for 2 h at 37 °C in darkness) and optical density (OD) was read against reagent blank with multi-well scanning spectrophotometer (ELISA reader, Model Expert 96, Asys Hitech, Austria) at the wavelength of 570 nm. The OD value of the study groups was divided by the OD value of the untreated control and presented as the percentage of control (as 100%).

Protein/ligand structure preparation and energy minimization

The crystal structure of DNA (PDB ID: 453D) was retrieved from RCSB protein data bank. The 3D structure of selected ligand was designed by hyperchem software. All water molecules and unknown atoms were removed from DNA.

Molecular docking

Molecular docking calculations were performed by AtoDock4.2 program package using the AutoDock empirical free energy function and the Lamarckian genetic algorithm with local search. First of all, water molecules were removed from initial structure of DNA and the missing hydrogen and Gasteiger charges were added to the system during the preparation of the DNA input file. AutoDock tools were applied for the preparation of coordinate files of ligand and DNA (PDBQT). Afterwards, pre-calculation of grid maps was performed using AutoGrid to save a lot of time during the docking. The docking calculation was done by locating a grid map with 70 70 110 Å points and a grid point spacing of 0.375 Å. The number of independent docking runs performed for each docking simulation was set to 200 with 250,000,000 energy evaluations for each run. The default values of program were used for other docking parameters. Molecular graphics were performed using VMD 1.9.2 software.

Results and discussion

Denaturation of DNA

According to the described method in the experimental section, a constant amount of DNA was titrated with different amount of complex. During DNA denaturation, the absorbance of chromophores such as phosphate groups will be changed at 258 nm. Sigmoidal Fig. 1 shows how this Pd complex unfolds DNA. It is clear that by increasing the metal complex concentrations, absorption is reduced. DNA has some groups such as phosphate, purine and pyrimidine that are usually suitable chromophores with sharp peak at 258 nm in UV–Vis spectroscopy. As Fig. 1 shows, during denaturation with metal complex if Pd complex stands in the new position, the absorbance of Ct-DNA will be changed. The absorbance of DNA with increasing concentrations of Pd complex decreases sharply due to the interaction of the hidden chromophore group of DNA with the complex.
Fig. 1

DNA denaturation by increasing the concentration of Pd complex at 27 and 37 °C

The concentration of complex in the midpoint of native to denatured transition of DNA, [L]1/2, was obtained in micromolar concentration. These values are 2.76 and 0.45 µmol/L at 27 and 37 °C, respectively. In fact, lower value means higher activity and maybe fewer side effects.

Using the DNA denaturation plot (Fig. 1) and Pace method [41, 50], the thermodynamic parameters were calculated and are provide in Table 1. Thermodynamic parameters mentioned in Table 1 are reported in the absence of the concentration of Pd complex and they are related to the stability of DNA.
Table 1

The thermodynamic parameters of DNA denaturation with Pd complex

Complex

T (°C)

[L]1/2 (µmol L−1)

Δ (H2O) (kJ mol−1)

Δ(H2O) (kJ mol−1)

ΔS° (H2O) (kJ mol−1 K−1)

[Pd(phendione)(isopentylglycine)]NO3

27

193

6.20

4.72

0.0156

37

145

6.25

0.0151

Unfolding equilibrium constant of natural DNA to the denatured state, K, and unfolding free energy of DNA, Δ, have been calculated at 27 and 37 °C. Figure 2 displays molar Gibbs free energy of DNA binding with Pd complex at both temperatures. This plot shows the values of Δ are decreased by adding metal complex to DNA due to decrease in the stability of DNA. The values ΔG° decrease with the addition of metal complex and by DNA–Pd complex formation. It shows the interaction between DNA and Pd ligand is a spontaneous process.
Fig. 2

Molar Gibbs free energy of DNA binding with Pd complex at 27 and 37 °C

In addition, the enthalpy for DNA denaturation, Δ, in the range of 27–37 °C is descending (Fig. 3), which indicates DNA interaction with complex is a spontaneous process. The positive ∆S° data show that the metal–DNA complex are more disordered than those of native DNA, because the entropy change is positive in the DNA denaturation processes. These data show that the metal–DNA complex can be deduced which shows a disturbed DNA structure due to the change of DNA conformation.
Fig. 3

Plot of the molar enthalpy of DNA interaction with Pd complex in the range of 27–37 °C

In addition, UV–Vis spectra of the Pd complex were obtained in the absence and presence of different concentrations of DNA (Fig. 4). The results show hyperchromic effect at 270 nm for [Pd(phendione)(isopentylglycine)]NO3, which means DNA helicity changed after groove binding of the Pd complex. The increment in absorbance intensity (hyperchromic effect) was observed when complex binds to DNA either by electrostatic interaction and groove binding or partial intercalation mode. The interaction of complex with DNA causes uncoiling of the helix structure of DNA; subsequently, hydrogen bonds between the complementary bases reduced, therefore, exposing more bases of the DNA and absorbance band increased [42, 43].
Fig. 4

Absorption spectra of 1 × 10−4 M of Pd complex (1) in Tris–HCl buffer–10 mM NaCl (pH 7.4). Arrow the absorbance changes upon increasing CT-DNA concentration (26). Inset plots of [DNA]/[εa − εf] vs. [DNA] for the titration of complex with DNA

Using spectroscopic titration data and Wolfe–Shimer equation \(\left(\frac{{[DNA]}}{{[\varepsilon _{{\text{a}}} - \varepsilon _{{\text{f}}} ]}} = \left( {\frac{{[DNA]}}{{[\varepsilon _{{\text{b}}} - \varepsilon _{{\text{f}}} ]}}} \right) + \frac{1}{{k_{{\text{b}}} [\varepsilon _{{\text{b}}} - \varepsilon _{{\text{f}}} ]}} \right)\), the intrinsic binding constant Kb can be calculated, where Ɛa is the apparent extinction coefficient (A/[complex]), Ɛf and Ɛb are extinction coefficients for the free complex (unbound) and complex in maximum bound form, respectively, Kb is calculated to be 115 mM−1 by the ratio of the slope to intercept of the plot in Fig. 5.
Fig. 5

The melting curve of DNA in the absence (open circle) and presence (closed circle) of Pd complex

Tm measurements

The double-helical structure of DNA is remarkably stable due to hydrogen bonding and base stacking interactions. By increasing the temperature, the helix is dissociated to single strand since heat damages the bonding forces. The value of Tm for DNA–Pd complex was determined by monitoring the absorbance at 260 nm. A change in Tm was observed due to interaction of Pd complex with DNA. Intercalative binding increases Tm up to 3–8 °C. According to Fig. 5, the value of Tm for DNA in the absence of complex is about 64 °C. However, the observed the value of Tm for DNA in the presence of complex is about 70 °C. The rise in Tm means the DNA double helix is stabilized through the interaction. The interaction of complex with DNA causes an increase in Tm and the result reveals intercalation binding mode of complex. Previously, the Tm value reported for DNA in the presence of [Pd(phen)(methylgly)]NO3, [Pd(phen)(propylgly)]NO3, and [Pd(phen)(amylgly)]NO3 are about 68.5, 70.5, and 71.0 °C, respectively. The interaction of Pd complexes with DNA causes an increase in Tm of Pd complexes and the result reveals intercalation binding mode of Pd complexes [44].

Fluorescence studies

Since the Pd complex in aqueous solution has no emission in the absence and the presence of DNA, fluorescence study of the interaction of synthesized Pd complex with DNA is not possible directly. Therefore, by adding the ethidium bromide (EB) to DNA, as a DNA-labeling agent, the emission is increased by intercalating EB in appropriate positions of DNA [45]. The EB–DNA solution was titrated with 1 mM solution of Pd complex and the intensity was decreased by replacement of complex with EB. Figure 6 shows the possibility of intercalation of Pd complex with DNA.
Fig. 6

Fluorescence emission spectra of EB (dotted), EB bound to DNA (1) quenching of EB–DNA by Pd complex (26)

Using phenomenon of fluorescence quenching data in Fig. 6, the dynamic or static quenching can be investigated according to Stern–Volmer equation \(\left( {\frac{{F_{0} }}{F} = 1 \, + \, K_{\text{q}} \tau [{\text{com}}] = 1 \, + \, K_{\text{sv}} [{\text{com}}]} \right)\), where F0 and F are the fluorescence emissions in the absence and presence of different concentrations of DNA, respectively, [com] is the concentration of Pd complex as the quencher and Ksv = kqτ0 is the Stern–Volmer quenching constants that are related to life time (τ0). The life time of a biomolecule is 10−8 s for calculating kq. The maximum value of kq for different quenchers with a protein is 2.0 × 1010 M−1 S−1 [46]. kq obtained is 1.16 × 108 M−1 S−1. Therefore, the nature of the quenching is dynamic, which means DNA complex formation is not because of quenching. Also the binding constant (Kf) and the number of binding sites (g) in the interaction of Pd complex and DNA can be determined by the following equation [47]: \(\log \left( {\frac{{F_{0} - F}}{F}} \right) = \log \;Ka + g\log [{\text{com}}],\) where F0 and F are similar to the aforementioned. Figure 7 shows that the values of Kf and g are 3.7 × 106 M−1 and 2.08, respectively.
Fig. 7

The Stern–Volmer plot for DNA–EB system, e = 471 nm, in the presence of Pd complex

Circular dichroism studies

Due to change in DNA conformation, DNA spectrum will be modified when Pd complex binds to DNA as a drug. The positive band is corresponding to base stacking helicity (273 nm) and the negative band is corresponding to right-hand helicity (264 nm). During every interaction of DNA with drug, these two bands are so sensitive. CD spectra of this Pd complex are shown in Figs. 8 and 9. Descending intensity in both positive and negative bands, without red or blue shift, shows that DNA binding of drug induces conformational changes, including the opening of the helix upon the covalent binding and the conversion from B-form DNA to C-form DNA [48] and suggests the possibility of intercalation and groove binding combination [48].
Fig. 8

Fluorescence Schatchard plot for binding of EB to DNA in the absence (1) and presence (2 to 6) of increasing the concentrations of Pd complex

Fig. 9

The CD spectrum of DNA (line), DNA complex with different concentrations (0.13, 0.23 and 0.33 µM) of Pd complex with r = [com]/[DNA]: 1.1, 1.2 and 2.7, respectively

Cytotoxic studies

The anti-proliferative and anticancer activity of the newly designed Pd(II) complex was checked against human model cancer cell line of HCT116 after 24 h of incubation. Therefore, in this study, various concentrations of Pd(II) complex ranging from 0 to 350 µM were used and results have been shown in Fig. 10. The 50% cytotoxic concentration (Cc50) of the Pd(II) complex was determined from Fig. 10 which shows the Cc50 value of 320 µM after 24 h of incubation. In addition, cytotoxicity results represent that the human colon cancer cell growth was significantly reduced after incubation with various concentrations of Pd(II) complex. It is clear that the synthesized Pd(II) complex presents a dose-dependent response to suppression on the growth of HCT116 cells.
Fig. 10

The growth suppression activity of the varying concentrations of Pd(II) complex on HCt116 cell line using MTT assay after 24 h of incubation time

Molecular docking

Table 2 presents docking energy, run and number of conformations in cluster for docking of [Pd(phendione)(isopentylglycine)]NO3 complex to DNA and Table 3 shows thermodynamic parameters resulting from the most negative luster rank (rank 1 in Table 2). The value of docking energy is −10.21 kcal/mol for the mentioned complex docked to DNA. The results retrieved from the docking study are in good agreement with those from experimental measurements and the negative value indicates a spontaneous process.
Table 2

Binding energy of [Pd(phendione)(isopentylglycine)]NO3 complex to DNA in kcal/mol

Cluster rank

Lowest binding energy (kcal/mol)

Run

No. in cluster

Mean binding energy (kcal/mol)

1

−10.12

52

14

−9.89

2

−10.12

36

75

−9.68

3

−9.89

183

75

−9.72

4

−9.62

42

7

−9.36

5

−9.62

146

5

−9.53

Table 3

Thermodynamic parameters for most negative cluster rank (rank 1 in Table 2 for the complex)

Thermodynamic parameters (kcal/mol)

Estimated free binding energy

−10.12

Estimated ligand efficiency

−0.37

Estimated inhibition constant (nM), Ki

37.87

Final intermolecular energy

11.02

Vdw + Hbond + desolve + energy

−6.43

Electrostatic energy

−4.59

Torsional free energy

0.89

Unbound system’s energy

−0.12

Both molecular docking and secondary structure studies in the circular dichroism spectrophotometry show the [Pd(phendione)(isopentylglycine)]NO3 drug interacted with DNA via minor groove binding. This complex has branched and long hydrocarbon chains which bind several nucleotides of DNA such as DA17, DA18, DT19, DC9, DG10 and DC11. In addition to VDW bonds, three hydrogen bonds have been formed between the nucleotides of DNA and ligand including DA17 (3.19 and 2.93 Å) and DC9 (2.74 Å) which have been showed as green dots in Figs. 11 and 12. The electrostatic surface results also confirmed that hydrophobic interaction is a predominate force during drug interaction with DNA, shown in white color (related to neutral groups) in the figures. The results are coherent with the fluorescence study results.
Fig. 11

[Pd(phendione)(isopentylglycine)]NO3 interacted with DNA via interaction and groove binding. a The structure of DNA, b the structure of ligand, and c the structure of DNA–ligand complex. d All nucleotides involved in the formation of three hydrogen bonds with the ligands (DA17: 3.19 and 2.93 Å, DC9: 2.74 Å). Hydrogen bonds are shown as green dots

Fig. 12

The schematic representation of [Pd(phendione)(isopentylglycine)]NO3 intercalated with nucleotides. Hydrogen bonds shown as red dots in the intercalated region between ligand and DNA

Conclusion

The new Pd complex of isopentyl-glycine and phendione ligands was synthesized and characterized by IR, UV and 1HNMR spectroscopy. Cytotoxicity study has shown that the designed Pd(II) complex represented its anti-proliferative and anticancer activity in dose-dependent responses with Cc50 value of 320 µM against human colon cancer cell line of HCT116 after 24 h of incubation time. In addition, thermodynamic and binding parameters were obtained by denaturation and titration plots that show high activity of Pd complex which is probably related to the presence of phendione in the complex structure. Using amino acid ligand, isopentylglycine, caused increased cytotoxic activity compared to other similar compounds [37, 49]. Furthermore, the fluorescence, CD and docking studies displayed intercalation and groove binding interaction of Pd complex with DNA. In fact, this Pd–phendione amino acid derivative with square planar geometry provides possible intercalative binding with DNA. Moreover, the presence of N, N- and N, O- donor ligand in Pd complex decreases the rate of hydrolysis, which in turn may lead to fewer side effects.

Notes

Acknowledgements

The authors gratefully acknowledge the financial support of this work by the Chemistry & Chemical Engineering Research Center of Iran.

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Copyright information

© SBIC 2017

Authors and Affiliations

  1. 1.Chemistry and Chemical Engineering Research Center of IranTehranIran
  2. 2.Department of Cell and Molecular Biology, Faculty of Biological SciencesKharazmi UniversityTehranIran

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