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BY 4.0 license Open Access Published by De Gruyter Open Access June 21, 2022

Copper(ii) complexes supported by modified azo-based ligands: Nucleic acid binding and molecular docking studies

  • Mamta Tripathi , Ashish Kumar Asatkar , Stalin Antony , Mrinal Kanti Dash , Gourisankar Roymahapatra , Rama Pande , Avijit Sarkar EMAIL logo , Fahad M. Aldakheel , Abdulkarim S. Binshaya , Nahed S. Alharthi , Ahmed L. Alaofi , Mohammed S. Alqahtani and Rabbani Syed
From the journal Open Chemistry
An erratum for this article can be found here:


Two new copper(ii) complexes [CuL1] (1) and [CuL2] (2) derived from azo-based ligands 2-hydroxy-5-p-tolylazo-benzaldehyde (HL1) and 1-(2-hydroxy-5-p-tolylazo-phenyl)-ethan-one (HL2) were synthesized. These two ligands and their metal complexes were characterized by elemental analysis, nuclear magnetic resonance (1H and 13C), infrared, and UV/Vis spectroscopic techniques. Spectroscopy and other theoretical studies reveal the geometry of copper complexes, and their binding affinity towards nucleic acids are major groove binding.

1 Introduction

Nucleic acids are fundamental biopolymers and the most significant genetic substances [1,2,3]. It can act as good binding ligands because nucleic acids have different binding modes for reversible or non-covalent interaction with transition metal complexes [4]. Hence, the design and synthesis of transition metal complexes is the subject of tremendous interest as it has strong binding efficiency to the nucleic acid and shows great screening for the development of new drugs [5]. Besides that, in the last few years, synthesis and physicochemical studies of transition metal complexes with azo-based (–N═N–) ligands have been given a lot of interest by chemists because of their versatile applications in different fields such as textile industries [6], analytical and catalytical activity, optical technology [7], and biofuel cell cathodes [8,9]. Azo dyes are also used in coloring agents for the food and cosmetic industries [10]. Bidentate-substituted azo-linked O,O donor ligands are very popular as they can coordinate with various transition metal ions [11]. The diazotization reaction of aniline or its derivate with salicylaldehyde has been a subject of interest in the area of pharmacology, catalyst, and sensors [12]. The metal ions can coordinate with various naturally occurring metalloproteins such as oxygen (O), nitrogen (N), and sulfur (S) donor atoms from the amino acid side chains. Synthesis and biological studies of copper-containing metal complexes increase because copper complexes act as a model for the active sites of different enzymes, and it has interesting properties such as anticancer, antitumor, antimicrobial, and antifungal activity [13,14,15]. On the basis of their huge applicability and potential biological activities, we recently synthesized, characterized, and studied the nucleic acid binding affinity of a series of azo-linked copper complexes [16]. Here, we present the synthesis and characterization of [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes containing O, O donor azo-linked ligands HL1 and HL2 (Chart 1). DFT calculation has been carried out to optimize copper complexes. Nucleic acid binding and molecular docking techniques have also been adopted to present the biological usefulness of newly synthesized complexes.

Chart 1
Chart 1

2 Experimental section

2.1 Reagents and materials

Substituted azo-aldehyde has been synthesized according to the modified procedure in our laboratory [17]. Chemicals and solvents of analytical grade and purified by the standard method and obtained from SRL, India, and Merck, India, were used. Calf thymus DNA (ct-DNA) and torula yeast (t-RNA) were obtained from Merck; ethidium bromide (EB), Tris–HCl, and NaOH were procured from dealers of Sigma Aldrich. The stock solution of ct-DNA was made in buffer (50 mM NaCl–5 mM Tris–HCl) at room temperature and retained a pH of 7.8 with 0.01 M HCl made by following the standard procedure. The ratio of the 1.8–1.9 absorbance value was retained at 260–280 nm. The stock solution of ct-DNA in the buffer has a ratio of 1.8–1.9:1 UV absorbance at 260–280 nm, pointing out that the DNA was sufficiently free from protein contamination [18]. The t-RNAPhe (yeast) concentration value was calculated spectrophotometrically using the molar extinction coefficient value (ε) of 6,900 M−1 cm−1 at 258 nm, expressed in terms of nucleotide phosphates. The ratio of the absorbance at 260–280 nm suggested that the sample was prevented from protein contaminations [16]. All experiments associated with t-RNA binding were done in citrate-phosphate (CP) buffer (1 mM [Na+], pH 7.0), containing 0.5 mM Na2HPO4, pH was adjusted using citric acid [19]. Spectroscopic-grade chemicals were used, and deionized and triple distilled water was used for making buffer and other solutions (Millipore India Pvt. Ltd., Bangalore, India).

2.2 Physical measurements

The elemental analyses (C, H, N) were completed using a Perkin-Elmer model 240C elemental analyzer. FT-IR analysis was performed in a Perkin-Elmer spectrum RX1 spectrometer. The solution’s electrical conductivity and electronic spectra were recorded using a Unitech type U131C digital conductivity meter (a solute concentration of about 10−3 M) and a Shimadzu UV 2450 UV-Vis spectrophotometer. For the study of UV-Vis spectral titrations, a Varian Cary 50 UV-Visible spectrophotometer (1.0 cm quartz cells specification). A Cary Eclipse fluorescence spectrophotometer (Varian, USA) (a xenon flash lamp with 1.0 cm quartz cells) was used for fluorescence spectral studies. UV-Vis absorption titration, fluorescence spectra, and ethidium bromide displacement method were done via following the reported literature [19]. Viscometric studies were performed via using a Ubbelohde viscometer. pH measurement was done using a Eutech Oakton digital pH meter coupled with a glass–calomel electrode having tarsons spin with a microcentrifuge (1.5 mL tube and rotation speed 6,000 rpm). Detailed experimental procedures are provided in the supplementary information. The optimization of structures of the complexes was done by density functional theory (DFT) calculations via employing the Gaussian 09 [20] program at the B3LYP/LanL2DZ level [21,22]. The ligand metal complexes were considered as the mono positive cationic complex and associated counter ions.

2.3 Preparation of azo-linked ligands (HL1–HL2)

The substituted azo-aldehyde ligands HL1 and HL2 were synthesized by the modified literature procedure mentioned in the literature [23]. In a beaker, p-toluidine (1.07 g, 10 mmol) was mixed with HCl (3 mL) and water (25 mL). The solution was cooled using a ice–water mixture and it has undergone diazotization with NaNO2 (0.97 g, 14 mmol) which was dissolved in water (5 mL) at the temperature between 0 and 5°C. To the solution of salicylaldehyde (1.06 mL, 10 mmol) or 2-hydroxy acetophenone (1.20 mL, 10 mmol) in water (20 mL) containing 10% NaOH solution (10 mL) was added to the cold reaction mixture for a period of 30 min and the reaction mixture was stirred for 1 h. After evaporation of the reaction mixture, a brown precipitate solid was obtained. The solid was isolated, washed with cold ethanol, and dried under vacuum over P4O10 (Scheme 1).

Scheme 1 
                  The proposed synthesis method of ligands L
                      and L
Scheme 1

The proposed synthesis method of ligands L 1 and L 2 .

2.3.1 2-Hydroxy-5-p-tolylazo-benzaldehyde (HL1)

Brown powder, yield: 2.2 g (95%). Elemental analysis for C14H12N2O2 (240.26 g/mol): Calc. C, 69.99; H, 5.03; N, 11.66. Found: C, 69.97; H, 5.01; N, 11.58%. NMR (300 MHz, CDCl3). Δ (ppm) = 1H, 11.33 (br, 1H, Ar-OH), 10.01 (s, 1H, Ar-CH═O), 8.17 (s, 1H, Ar-CH), 7.82 (d, 2H, Ar-CH), 7.33–7.09 (m, 5H, Ar-CH), 2.37 (s, CH3).13C, 196.20 (C═O), 163.32, 150.13, 145.64, 130.31, 129.45, 128.66, 122.40, 119.95, 118.14, 213. IR (cm−1): 3,357 ν(O–H), 1,621 ν(C═O), 1,697 and 1,445 ν(–N═N–, cis and trans), 1,323 ν(C–O), 1,168, 1,119, 801, 766, 686, 548, 498. UV-Vis (DMF); λ max = 339 nm.

2.3.2 1-(2-Hydroxy-5-p-tolylazo-phenyl)-ethan-one (HL2)

Brown powder, yield: 2.19 g (86.2%). Elemental analysis for C15H14N2O2 (254.11 g/mol): Calc. C, 70.85; H, 5.55; N, 11.02. Found: C, 70.75; H, 5.52; N, 10.98%. NMR (CDCl3, δ ppm): 1H, 13.31 (s, 1H, OH), 8.72 (s, 1H, aromatic CH), 7.99 (d, 2H, aromatic CH), 7.51–6.90 (m, 5H, aromatic CH). 13C, 196.18 (C═O), 163.38, 152.00, 132.78, 130.23, 127.60, 127.14, 122.27, 77.11. IR (cm−1): 3,188 ν(O–H), 1,659 ν(C═O), 1,602 ν(C═C), 1,574 and 1,479 ν(–N═N–, cis and trans), 1,278, 1,170, 1,115, 842, 764, 691, 581, 486. UV-Vis (DMF); λ max = 355 nm.

2.4 Synthesis of copper complexes

To a stirred methanolic solution, azo-linked aldehyde of HL1 (0.48 g, 2 mmol) or HL2 (0.508 g, 2 mmol) in 20 mL methanol was added to Cu(ClO4)2·6H2O (0.37 g, 1 mmol) in MeOH (15 mL) solutions. After 10 min, triethylamine (0.5 mL, 3.58 mmol) were added, and the reaction mixtures were stirred for another period of 1 h. After cooling and evaporating in air, brown precipitate separated out. The deep brown solid was isolated by filtration, washed with water, and dried under vacuum over P4O10.

2.4.1 [Cu(L1)2] (1)

Brown powder, Yield: 83%. Anal. calc. for C28H22N4O4Cu1 (542.04 g/mol): Calc. C, 62.04; H, 4.09; N, 10.34. Found: C, 62.01; H, 3.98; N, 10.31%. Selected FT-IR bands (cm−1): 3,007 (br), 1,613 (s), 1,450 (s), 1,326 (m), 1,270 (m), 1,105(s), 910 (s), 528 (m). Molar conductance, ΛM: (DMF solution) 5.2 ohm−1 cm2 mol−1. UV-Vis (DMF); λ max = 370 nm.

2.4.2 [Cu(L2)2] (2)

Brown powder, yield: 78%. Elemental analysis for C30H26N4O4Cu1 (570.10 g/mol): Calc. C, 63.20; H, 4.60; N, 9.83. Found: C, 63.18; H, 4.57; N, 9.79%. Selected FT-IR bands (cm−1): 3,039 (br), 1,589 (s), 1,455 (m), 1,401 (s), 1,302 (s), 1,235 (m), 520 (m). Molar conductance, ΛM (DMF solution): 6.0 ohm−1 cm2 mol−1. UV-Vis (DMF); λ max = 362 nm.

2.5 DFT calculations

The DFT technique was used for computational optimization. To get insight into the stable ground state geometry, the proposed complex structures [17] at the B3LYP level of theory with LANL2DZ in the Gaussian 16 program [24] correlate with analytical data. The zero imaginary frequency value proves their presence in the minima on the potential energy surface. The optimized geometry was generated using the Gauss view-6 program [25].

2.6 Molecular docking studies

AutoDock Tools 1.5.6v (ADT) installed on the Ubuntu 18.04 LTS operating system was used to analyze the docking simulation between the new two copper(ii) complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) derived from azo-based ligands the 2-hydroxy-5-p-tolylazo-benzaldehyde (L1) and 1-(2-hydroxy-5-p-tolylazo-phenyl)-ethan-one (L2) ligands and the DNA/RNA [26,27]. The 3D structure of a B-DNA dodecamer with the resolution of 1.9 Å (PDB ID: 1BNA) was retrieved using the data bank of the protein ( All complexes were structurally optimized, as discussed above.

3 Result and discussion

3.1 Spectral characterization

For characterization of modified azo-based ligand and their metal complexes, we adopted different spectroscopic techniques via NMR, UV/Vis, IR spectroscopy. The NMR data (1H and 13C) of the ligands were observed in DMSO-d 6 solvents. All the data are provided in the experimental section, and spectra are in the supporting information (Figures S1–S4). The 1H NMR spectrum of ligand HL1 displayed a signal at 11.33 ppm or 10.01 ppm which is due to the protons of the phenolic and aldehyde, respectively. The case of HL2 signal at 13.31 ppm is due to phenolic proton. In the 13C NMR, spectrum signals appeared at 196.2 and 196.18 ppm due to the carbonyl group (>C═O) of ligands HL1 and HL2, respectively. These ligands were confirmed by carefully assessing these NMR data with the previously reported similar azo-based ligands [13].

Selected IR data and spectra have been given in Table 1 and Figures S5–S8. The characteristic peak in the range of 1,445–1,450 and 1,455–1,479 cm−1 are observed due to the azo group present in ligands and metal complexes [23]. Broad peaks around 3,188–3,357 cm−1 are assigned to ν(O–H) vibration of ligands which are absent in metal complexes because of coordination of the OH group [28]. Stretching vibration of the C═O group of the ligands HL1 and HL2 shifted to the lower wavenumber values of the complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) from 1,621 to 1,613 cm−1 and 1,659 to 1,589 cm−1, respectively, due to complex formation. New vibration bands (not obtained in the spectrum of the ligand) appeared around 520–528 cm−1, corresponding to M–O vibrations, indicate the involvement of O atoms in coordination with the metal center [15,28]. After complex formation, the carbonyl group ν(C═O) stretching shifted to the lower wavenumber values of the complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) from 1,636 to 1,621 cm−1 and 1,666 to 1,632 cm−1 respectively [29].

Table 1

Characteristic IR absorption bands for ligands and its complexes

Compound ν(–N═N–) ν(O–H) ν(C═O) ν(Cu–O)
HL1 1,445 3,357 1,621
HL2 1,479 3,188 1,659
[Cu(µ-L1)2] (1) 1,450 1,613 528
[Cu(µ-L2)2] (2) 1,455 1,589 520

Absorption spectra of ligands HL1 and HL2 were observed in MeOH, and complexes were observed in DMF solution (Figure 1). For the ligands, two absorption bands at 355 and 339 nm were appeared due to the π → π* intra-ligand transitions. After complex formation, the absorption band shifts to a higher wavelength region from 355 to 362 nm for complex [Cu(L1)2] (1) and 339 to 370 nm for complex [Cu(L2)2] (2), respectively [10].

Figure 1 
                  Absorption property of complexes and ligands in DMF solution.
Figure 1

Absorption property of complexes and ligands in DMF solution.

Powder XRD patterns of Cu(ii) complexes recorded in the range (2 h = 0–80°) were shown in Figure S9a and b. XRD patterns of the metal complexes show the sharp crystalline peaks indicating their crystalline phase. The average crystallite size (dXRD) of the complexes was calculated using Scherer’s formula10a. The precipitates of Cu(ii) complexes have an average crystallite size of 81 and 86 nm, respectively.

3.2 Geometry optimization of copper complexes

A neutral complex of Cu(ii) forms with anionic ligands (phenoxide anionic) (Figures 2 and 3). Here, two ligands react and form square planner complexes with molecular formulas C28H22Cu1N4O4[Cu(L1)2] (1) and C30H26Cu1N4O4[Cu(L2)2] (2); both have no symmetry except for C1. Selective bond parameters are provided in Table 2. The bond length between Cu–Ophenolic varies between 1.918 Å (complex 1) to 1.911 Å (complex 2) and that of Cu–Ocarboxylic 1.983 Å (for complex 1) to 1.969 Å (complex 2). The presence of an additional methyl group in complex 2 (+I effect) increases the electron density around the ‘O’ atom and favors the Cu–O bond stronger with a lower bond distance (1.969 Å) compared to complex 1 (1.983 Å). Related bond angles surrounding the Cu atom are in right angle (varies ± 0.54°) and the dihedral angles witnessed deduction in perfect square planner geometry of the complexes similar to our previous report [15] of O,O donor ligands in comparison to similar type recent report of azobenzene–anthraquinone Schiff base copper complexes [17], where the ligands are the N,O donor, the (Cu–O) and (Cu–N) bond length are shorter than the present study, and the bond angles pivoting to the Cu center varies ±2–4° from right angle showing a distortion in square planar geometry.

Figure 2 
                  Optimized structure of Complex 1.
Figure 2

Optimized structure of Complex 1.

Figure 3 
                  Optimized structure of Complex 2.
Figure 3

Optimized structure of Complex 2.

Table 2

Selective bond parameters of optimized structures

Parameters Complex 1 Complex 2
Bond length (Å) Cu–Ocarbo 1.983, 1.983 1.969, 1.969
Cu–Ophen 1.918, 1.918 1.911, 1.911
Bond angle (°) O–Cu–O 90.52, 90.52 89.46, 89.46
89.48, 89.48 90.54, 90.54
Dihedral angle (°) O–O–Cu–O 180.00, 180.00 179.98, 179.98
179.99, 179.99 179.97, 179.97

3.3 Nucleic acid binding studies

3.3.1 Binding studies via electronic absorption spectroscopy

Cu(ii) metal-based two novel complexes were titrated against increasing concentration of nucleic acid. Cu(ii) complexes are associated with the d9 state of metal ion, and the significance of the first d–d transition, second intra-ligand transition, and lastly metal-based ligands transition was seen. A few specific electronic transition includes a peak at 257–356 nm, which might be due to intra-ligand transition (π → π*) and next broader peak appears around 320–400 (n → π*) nm was most probably due to ligand to metal charge transfer (LMCT) transition [30,31]. In both the complex aliquots upon successive addition of genetic material (DNA/RNA) showed hyper chromic shift, possibly due to the forceful incorporation of [Cu(L1)2] (1) and [Cu(L2)2] (2) complex into the genomic sequences. The aromatic ring of complexes adjacently linked with the curvy groove region of the DNA helix, aromatic ring of ligands binds with DNA in buffer solution through various weak non-covalent force of attraction like van der Waals force of attraction or it might be hydrogen bonding. Hyperchromic shift with slightly red shift around 10 nm shows the resemblance of either electrostatic [32] or groove interaction [33], which occurs due to the surface attachment of complex molecules with DNA via weak force of attraction [34], or it may be due to the interaction of the Cu(ii) complex with the twisting turn region of nucleic acid. In Figure 4(a) and Figure S10(a), the [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes showed interaction with ct-DNA, and the spectral band was observed at around 250 and 355 nm, (red shift 250–257), respectively; and a sharp incremented pattern can be observed corresponding to the π → π* in pyrimidine and purine ring systems of DNA, while the band at around 360 nm (corresponding to the n → π*) displayed poor hypochromic shifting for both the complexes. The K b values calculated via linear fittings of the obtained experimental data were found to be 3.99 ± 0.2 × 103 M−1 for [Cu(L1)2] (1) complex and 3.25 ± 0.2 × 103 M−1 for [Cu(L2)2] (2) complex. In Figure 3(b) and Figure S10(b) graph of the [Cu(L2)2] (2) complex, was shown with increasing concentration of tRNA; the appreciable extent of hyperchromic shifting was observed, with the spectral band around 260 nm and at around 365 nm. The passage structure of tRNAPhe is an extremely complex structure to study its inherent interaction; the pattern of UV titrations suggests complexes were successful in binding with tRNA biomolecules by electrostatic surface binding with partial inserting itself into the RNA groove region. The K b, values calculated via linear fittings of the observed experimental data are [Cu(L1)2] (1) is K b tRNA value [Cu(L2)2] (2) is 6.12 ± 0.3 × 103 M−1, [Cu(L2)2] (2) is 8.81 ± 0.5 × 102 M−1.

Figure 4 
                     UV-Vis spectra of (a) 1-ct-DNA (b) 2-t-RNA with constant increasing concentration of ct-DNA and t-RNA (0–125 mL) at 298 K.
Figure 4

UV-Vis spectra of (a) 1-ct-DNA (b) 2-t-RNA with constant increasing concentration of ct-DNA and t-RNA (0–125 mL) at 298 K.

3.3.2 Competitive binding studies via fluorescence spectroscopy

For the identification of the actual mode of binding the competitive binding assay method is used. Using ethidium bromide (EB) serve as a probe for intercalation, [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes undergoing for binding screening were added in EB-DNA/EB-RNA adduct aliquot [35]. In Figure 5(a) and (b) and Figure S11(a) and (b) 1 for both types of polynucleotides (DNA/tRNA); fluorescence emission spectra appeared to be in alleviated form often resembles non-competitive binder for EB–nucleic acid adduct [36,37]. The inefficiency of displacing EB from EB–nucleic acid adduct eradicate the possibility of intercalation mode of binding [38,39]. Groove or surface mode of interaction marked its dominance [40]. Present scenario of result, considering UV analysis helps in establishing a major groove as the binding mode for DNA [19]. The Stern–Volmer constant, K sv was calculated as for [CuL1] as 8.55 ± 0.2 × 103 M−1 and [CuL2] as 1.02 ± 0.4 × 103 M−1. Where while focusing on the tRNA biomolecule, a similar incremented spectral pattern was repeated, as it has a well-known that the structure of tRNA is an extremely entangled structure, comprised of a specific region of a self-coiling double helix, loop region, and bared ends. A complex need to compete in that particular region, in the present case that competence was not seen. Hence, in the case of tRNA too, bindings were concluded as a major groove [41]. The Stern–Volmer constant, K sv, was calculated for [Cu(L1)2] (1) as 1.04 ± 0.2 × 104 M−1 and for [Cu(L2)2] (2) as 6.76 × 103 ± 0.4 M−1.

Figure 5 
                     Emission spectra of EB bound to DNA where amounts of complexes CuL1 was higher (a) and (b) emission spectra of EB bound to tRNA in the presence of increasing amount of complexes 1. Inset: Stern–Volmer plots (Fo/F vs [1/2]) of fluorescence titration.
Figure 5

Emission spectra of EB bound to DNA where amounts of complexes CuL1 was higher (a) and (b) emission spectra of EB bound to tRNA in the presence of increasing amount of complexes 1. Inset: Stern–Volmer plots (Fo/F vs [1/2]) of fluorescence titration.

3.3.3 Binding studies via the viscometric method

Usually, in the case of intercalation, relative viscosity seems to be elevated based on the fact that intercalation leads to the insertion of a molecule into the base pairs of a macromolecule, which cause an increase in the length of DNA/RNA, hence viscosity increases [42,43,44]. Uncertainties too found in a few cases, but in the present work, it is observed that a decrease in the relative viscosity was seen as compared to the relative viscosity of DNA alone. In the groove mode of interaction, the complex makes an effort to embed itself into the curvy region of the DNA ladder, forcibly addition adds bulkiness to the DNA structure which ultimately leads to a decrease in viscosity of DNA. In Figure 6(a), it is found that the consecutive addition of CuL1 and CuL2 complexes into DNA induces a reduction in relative viscosity and suggests the probability of groove binding [45]. The reduction in relative viscosity is probably due to sideways overlapping or embedding it, causing nick or break on a double helical structure which interns result in a reduction in relative viscosity. Similar observation was found in the reported literature for the [Ru(phen)3]2+ (phen = 1,10-phenanthroline) complex [46,47]. The reduction in relative viscosity shows the existence of complexes is lesser, as observed in reported intercalation with EB [29]. Whereas the elevation of relative viscosity too accounts for groove binding, but the extent of finding such observation is less [48,49]. In the end, it can be concluded that both [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes merge as a major groove binder for both ct-DNA and tRNA resulting in increasing the relative viscosity, which probably due to the bulkiness of complexes found attached with the groups enforce the insertion into deep grudge of tRNA, leading to breaking or making cuts into the coiled of tRNA, breakage provides gaps or way to enter into the strands of tRNA resulting in partial insertion which increase the relative viscosity of complex. In Figure 5(b), it was observed that successive addition of complex in higher concentration leads to an increase in viscosity for ct-DNA, whereas in the case of tRNA, viscometric inference is not important due to the complicated structure of RNA. Hydrodynamic measurements clearly showed a rise in relative viscosity; the reason might be loop, or various regions of complementary base pairs may serve as a binding region which leads to heavier tRNA–[Cu(L1)2] (1) and [Cu(L2)2] (2) complex association [50].

Figure 6 
                     Effect of the Cu(ii) complexes ([Cu(L1)2] (1) and [Cu(L2)2] (2)) on the relative viscosities of (a) ct-DNA and (b) tRNA at 30°C.
Figure 6

Effect of the Cu(ii) complexes ([Cu(L1)2] (1) and [Cu(L2)2] (2)) on the relative viscosities of (a) ct-DNA and (b) tRNA at 30°C.

3.3.4 Quantum efficiency

Quantum efficiency (Q) subsidizes the magnitude of interaction of [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes to ct-DNA/tRNA. A graphical plot of absorbance versus the inverse of DNA/tRNA molar concentration provides an exponential plot with a quantum efficiency value of Q > 1 was calculated, which recommends an increment in the energy level of the associated ligands. Q > 1 is the symbol of incrementing fluorescence spectral intensity along with higher detention of fluorescence energy of the associated ligand bound to [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes due to screening which is not beyond the vicinity of the binding site from solvent quenching [14,15].

3.3.5 Molecular docking

Auto Dock (4.0) software was used for Molecular Docking analysis with two receptor [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes with ligand quadruplex DNA (PDB id: 1 BNA and RNA [PDB id-1tra]). Docking was performed by selecting the nucleotide by speculating the binding with a selected sequence with minimum steric hindrance. A lower value of binding free energy is preferably favored for the most potent molecule where biomolecule (DNA/RNA) [51,52,53,54]. Table 3 comprises of values of binding energy, and higher negative values suggest a greater extent of binding. Experimental analysis complements the theoretical binding, which predicts a major groove as binding mode [51,52,53]. Figure 7(a) and Figure S12(a) show tate 1 docked into the double helix of DNA. It was also observed that the binding modes between the complexes and G-quadruplex DNA follows a combination pattern of electrostatic/metal phosphate interactions (between the metal and DNA’s backbone), p–p end stacking (between the ligand and the G-quartet), and hydrophobic interactions. [Cu(L1)2] (1) and [Cu(L2)2] (2) both the complexes show their specificity towards major groove binding in the case of DNA binding with residues of oxygen, nitrogen with a ligand efficiency of 0.34 and 0.28. The relative binding energies of both the complexes docked into DNA are −12.63 and −10.93 kcal/mol, respectively. In Figure 6(b) and Figure S12(b) docked structures of both the complexes are shown docked into the polynucleic strand of tRNA. In this case, [Cu(L1)2] (1) and [Cu(L2)2] (2) complexes show the electrostatic mode of interactions with partial groove binding with tRNA leading to nicking or breaking the complex RNA molecules into small fragments, with precisely attaching to oxygen and nitrogen of nucleotides bases [26]. Both the formed complexes bind exactly over the same region of the RNA [55,56]. The relative binding energy of both the complexes is obtained as −8.86 and −8.54 kcal/mol [57,58,59].

Table 3

Binding interaction of complex with biomolecules

Ligand Protein/DNA Binding residues Binding energy (kcal/mol) Vdw_hb_desolv_energy (kcal/mol) Inhibition constant RMSD (Ǻ) Ligand efficiency
1 1bna DC‘9/O4’, DT‘8/O2, DA‘18/N3, DT‘19/O4’, DT‘20/O3' −12.63 −14.46 550.12 (pM) 24.8 0.34
2 DT‘19/O2, DT‘20/O3’/O4' −10.93 −12.69 9.79 (nM) 24.83 0.28
1 1tra U‘7/O2/O2’/O3’, U‘68/O2/O2' −8.66 −10.46 446.88 (nM) 42.17 0.23
2 U‘7/O2’, G‘15/N7, C‘48/O3’, A‘66/N3 −8.54 −10.28 550.66 (nM) 47.5 0.22
Figure 7 
                     Molecular docked model of 1(a) with DNA dodecamer duplex and (b) with RNA nucleotide.
Figure 7

Molecular docked model of 1(a) with DNA dodecamer duplex and (b) with RNA nucleotide.

4 Conclusion

Present work deals with the synthesis of two novel complexes of Cu in a +2 oxidation state. Characterization experimentally and theoretically analyzed and reported. Both the complexes were tested for drug-likeliness molecules by investigating their binding behavior with nucleic acids (DNA/RNA). All the synthesized complexes were checked for their applicability as nucleic acid binders. Experimentation techniques followed by computation analysis predict specific binding interaction of complexes at a precise region of DNA and RNA. In the case of DNA, conclusion were drawn by studying the experimentation results retrieved from UV absorption spectroscopy, fluorescence spectroscopy, viscometry which interns related with molecular docking results as major groove to be interactional mode of binding. Major groove appears to be wider opened pocked for incoming molecule facilitating inward pushing of protruding atom of the complex via binding force of attraction exist between polar atoms. While in the case of t-RNA, it seems that the insertion of complex molecules leads to distortion in a bimolecular arrangement. Electrostatic interaction via atomic insertion of the complex into t-RNA seems to be a mode of binding. Firmly, analysis of experimentation with computational analysis concludes electrostatic binding via partial groove as the mode of binding. [Cu(L1)2] (1) and [Cu(L2)2] (2) both complexes show potency as drug-like molecules, and outcomes successfully support them for further screening.

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Authors extend their appreciation to Researchers Supporting number (RSP2022/R506) at King Saud University, Riyadh , Saudi Arabia for Funding this work. Avijit Sarkar is thankful to the Bhairab Ganguly College and Science & Technology and Biotechnology (DSTBT), Government of West Bengal (Sanc. G.O. no: 244(Sanc) ST/P/S&T/15G-35/2017).

  1. Funding information: Fahad M.Aldakheel, extend their appreciation to Researchers Supporting Project number (RSP2022/R506), King Saud University, Riyadh, Saudi Arabia, for funding this work. Avijit Sarkar is thankful to the Bhairab Ganguly College and Science & Technology and Biotechnology (DSTBT), Government of West Bengal Sanc. G.O. no: 244(Sanc.)/ST/P/S&T/15G-35/2017).

  2. Author contributions: Avijit Sarkar contributes to the synthesis of metal complexes. Mamta Tripathi and Rama Pande focused on biological studies Ashish Kumar Asatkar and Stalin Antony contributed to molecular docking studies. Mrinal Kanti Dash and Gourisankar Roymahapatra expertise in DFT studies on the synthesized metal complexes. Fahad M. Aldakheel, Abdulkarim S. Binshaya, Nahed Alharthi, Ahmed L. Alaofi, Mohammed S. Alqahtani, and Rabbani Syed are support the funding for publication.

  3. Conflict of interest: There is no conflict of interest.

  4. Data availability statement: The data sets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

  5. Informed consent: Yes, and written concern already provided by the corresponding author.

  6. Ethical approval: The conducted research is not related to either human or animal use.

  7. Supporting information available: NMR, FTIR, UV-Vis spectra, DNA binding experiments, and molecular docked model of the complexes (Figures S1–S12) are given in Supplementary Information and are available free of charge via the internet.


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Received: 2022-02-28
Revised: 2022-03-29
Accepted: 2022-05-03
Published Online: 2022-06-21

© 2022 Mamta Tripathi et al., published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

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