Spectroscopic and In Silico Evaluation of Interaction of DNA with Six Anthraquinone Derivatives

Multifunctional red-emissive AIEgens as DNA-intercalating ligands: dual sensing of pH and viscosity accompanied by tissue imaging

The best antimicrobials and cancer therapies intercalate DNA-binding compounds to target DNA-processing proteins. We developed a DNA intercalator ligand that addresses the aggregation to speed up the development of novel intercalating medications. This DNA-intercalating ligand allows cellular imaging with little background interference due to its aggregation-induced emission (AIE) and colorimetric pH-responsiveness. These properties make it a versatile biosensor. The ligand exhibits robust intercalative binding with DNA at a 52.6 nM concentration and a high affinity of 55.46 × 106 M-1, ensuring sensitivity to low DNA concentrations. By changing its emission intensity and spectrum features with viscosity, the ligand may sense its microenvironment's physical parameters. It also changes color when pH changes, making pH monitoring easy and noticeable. We studied its DNA interaction using absorbance, fluorescence, and circular dichroism spectroscopy. To determine the mechanism, we performed dye-displacement tests, melting temperature investigations, and iodide quenching. Red fluorescence, high-affinity DNA intercalation, aggregation-induced emission (AIE), viscosity sensitivity, and pH-dependent colorimetric response make this ligand a promising candidate for DNA-targeted imaging and pH-sensitive biosensing in biological and environmental applications. Plant cell tissue imaging has also proved successful.

Copper-mediated DNA damage caused by purpurin, a natural anthraquinone

Background

Purpurin (1,2,4-trihydroxy-9,10-anthraquinone), a natural red anthraquinone pigment, has historically been used as a textile dye. However, purpurin induced urinary bladder tumors in rats, and displayed a mutagenic activity in assay using bacteria and mammalian cells. Many carcinogenic dyes are known to induce bladder cancers via DNA adduct formation, but carcinogenic mechanisms of purpurin remain unknown. In this study, to clarify the mechanism underlying carcinogenicity of purpurin, copper-mediated DNA damage induced by purpurin was examined using ³²P-labeled DNA fragments of human genes relevant to cancer. Furthermore, we also measured 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG), an indicator of oxidative DNA damage, in calf thymus DNA.

Results

Purpurin plus Cu(II) cleaved ³²P-labeled DNA fragments only under piperidine treatment, indicating that purpurin caused base modification, but not breakage of the DNA backbone. In the absence of Cu(II), purpurin did not induce DNA cleavage even with piperidine treatment. Purpurin plus Cu(II) caused piperidine-labile sites predominantly at G and some T residues. Bathocuproine, a Cu(I) chelator, completely prevented the occurrence of piperidine-labile sites, indicating a critical role of Cu(I) in piperidine-labile sites induced by purpurin plus Cu(II). On the other hand, methional, a scavenger of a variety of reactive oxygen species (ROS) and catalase showed limited inhibitory effects on the induction of piperidine-labile sites, suggesting that ROS could not be major mediators of the purpurin-induced DNA damage. Considering reported DNA adduct formation by quinone metabolites of several carcinogenic agents, quinone form of purpurin, which is possibly generated via purpurin autoxidation accompanied by Cu(I)/Cu(II) redox cycle, might lead to DNA adducts and piperidine-labile sites. In addition, we measured contents of 8-oxodG. Purpurin moderately but significantly increased 8-oxodG in calf thymus DNA in the presence of Cu(II). The 8-oxodG formation was inhibited by catalase, methional and bathocuproine, suggesting that Cu(I)-hydroperoxide, which was generated via Cu(I) and H₂O₂, caused oxidative DNA base damage.

Conclusions

We demonstrated that purpurin induces DNA base damage possibly mediated by Cu(I)/Cu(II) redox cycle both with and without ROS generation, which are likely to play an important role in its carcinogenicity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41021-022-00245-2.

Spectroscopic and docking molecular study of new anticancer Pt complex binding with human serum albumin

After synthesizing and identifying the nature of the new complex based on platinum metal, [Pt(NH₃)₂(butylgly)]NO₃, the interaction of this complex with human serum albumin (HSA) was performed by spectroscopy and molecular docking methods at two temperatures of 27 and 37 °C and under physiological conditions of the body. The toxicity test of this complex was performed on the MCF-7 cell line (IC₅₀ = 300 µM). Enthalpy, entropy, Gibbs free energy, binding constant, number of complex binding sites on the HSA, Scatchard diagrams, Hill coefficient, and Hill constant were calculated and then plotted via UV/Vis. According to the Gibbs free energy obtained at two temperatures of 27 and 37 °C (-20.6, -21.2 kJ mol^-1), the interaction was done spontaneously. Moreover, the melting temperature of human serum albumin with this complex; and the kinetics of this interaction (the second-order) were calculated. Using fluorescence at three temperatures of 25, 27, and 37 °C, the binding constant (2.9 × 10⁴, 1.0 × 10⁴, and 5.7 × 10³ M^-1), the quenching constant, average aggregation number of HSA, and the number of binding sites of the complex on the protein were obtained. As well, the static quenching mechanism was also observed. Molecular docking results showed that the site of binding of this complex to the HSA, is the site II subdomain IIIA, and the hydrogen and hydrophobic bonds are superior.

Kinetic and Thermodynamic Investigation of Human Serum Albumin Interaction with Anticancer Glycine Derivative of Platinum Complex by Using Spectroscopic Methods and Molecular Docking

In this paper, a new anticancer Pt (II) complex, cis-[Pt (NH₃)₂(tertpentylgly)]NO₃, was synthesized with glycine-derivative ligand and characterized. Cytotoxicity of this water-soluble Pt complex was studied against human cancer breast cell line of MCF-7. The interaction of human serum albumin (HSA) with Pt complex was studied by using UV-Vis, fluorescence spectroscopy methods, and molecular docking at 27 and 37 °C in the physiological situation (I = 10 mM, pH = 7.4). The negative [Formula: see text] and positive [Formula: see text] indicated that electrostatic force may be a major mode in the binding between Pt complex and HSA. Binding constant values were obtained through UV-Vis and fluorescence spectroscopy that reveal strong interaction. The negative Gibbs free energy that was obtained by using the UV-Vis method offers spontaneous interaction. Fluorescence quenching the intensity of HSA by adding Pt complex confirms the static mode of interaction is effective for this binding process. Hill coefficients, n_H, Hill constant, k_H, complex aggregation number around HSA, <J>, number of binding sites, g, HSA melting temperature, T_m, and Stern-Volmer constant, k_SV, were also obtained. The kinetics of the interaction was studied, which showed a second-order kinetic. The results of molecular docking demonstrate the position of binding of Pt complex on HSA is the site I in the subdomain IIA.

Studies on the Interaction of [SnMe2Cl2(bu2bpy)] Complex with ct-DNA Using Multispectroscopic, Atomic Force Microscopy (AFM) and Molecular Docking

The interaction of SnMe₂Cl₂(bu₂bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV-Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe₂Cl₂(bu₂bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859 nm were observed by using AFM for Sn(IV) Complex-DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO₂ group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe₂Cl₂(bu₂bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA-complex mixture confirmed the experimental results.

Novel isothiacalothrixin B analogues exhibit cytotoxic activity on human colon cancer cells in vitro by inducing irreversible DNA damage

Preliminary cytotoxic analysis of sulphur containing isosteric analogues of calothrixin B identified the useful anti-tumour activity of thia/isothiacalothrixin B which necessitated it’s biological evaluation in colon and lung cancer cell lines. The isothia analogues induced cytotoxicity of HCT116 in a time-dependent manner and inhibited the clonogenic survival of HCT116 and NCI-H460 cells in a dose-dependent manner comparable to the standard anti-cancer drug camptothecin. Herein employing flow cytometry, we demonstrate that isothiacalothrixin B analogues inhibited proliferation of colon cancer cells by the arrest of cells in S and G2/M phases over a period of 48 hours at a concentration of 5 μM. Our results also suggest that the cytotoxicity of thia analogues of calothrixin B is partially mediated by induction of cellular DNA strand breaks. The UV-Vis spectroscopic studies with CT-DNA revealed groove binding for calothrixin B and its thia analogues wherein subsequent in silico molecular modelling studies indicated preferential binding to the AT-rich regions of minor groove of DNA. Furthermore, thiacalothrixin B caused transcriptional activation of p21^waf1/cip1 promoter and upregulation of its protein levels independent of p53. The induction of DNA damage response pathway leads to apoptosis in isothiacalothrixin B but not in thiacalothrixin B treated cells. The isothia analogues SCAB 4 induced DNA strand breaks and cell cycle arrest even after treatment for a short period (i.e., 4 hours) and the cell cycle effects were irreversible. For the first time, this study provides detailed cellular effects on the potential use of isothiacalothrixin B analogues as cytotoxic agents.

Multihydroxy-Anthraquinone Derivatives as Free Radical and Cationic Photoinitiators of Various Photopolymerizations under Green LED

Multihydroxy-anthraquinone derivatives [i.e., 1,2,4-trihydroxyanthraquinone (124-THAQ), 1,2,7-trihydroxyanthraquinone (127-THAQ), and 1,2,5,8-tetrahydroxyanthraquinone (1258-THAQ)] can interact with various additives [e.g., iodonium salt, tertiary amine, N-vinylcarbazole, and 2-(4-methoxystyryl)-4,6-bis(trichloromethyl)-1,3,5-triazine] under household green LED irradiation to generate active species (cations and radicals). The relevant photochemical mechanism is investigated using quantum chemistry, fluorescence, cyclic voltammetry, laser flash photolysis, steady state photolysis, and electron spin resonance spin-trapping techniques. Furthermore, the multihydroxy-anthraquinone derivative-based photoinitiating systems are capable of initiating cationic photopolymerization of epoxides or divinyl ethers under green LED, and the relevant photoinitiation ability is consistent with the photochemical reactivity (i.e., 124-THAQ-based photoinitiating system exhibits highest reactivity and photoinitiation ability). More interestingly, multihydroxy-anthraquinone derivative-based photoinitiating systems can initiate free radical crosslinking or controlled (i.e., reversible addition-fragmentation chain transfer) photopolymerization of methacrylates under green LED. It reveals that multihydroxy-anthraquinone derivatives can be used as versatile photoinitiators for various types of photopolymerization reactions.

Synthesis and Biological Evaluation of Calothrixins B and their Deoxygenated Analogues

A series of calothrixin B (2) analogues bearing substituents at the 'E' ring and their corresponding deoxygenated quinocarbazoles lacking quinone unit were synthesized. The cytotoxicities of calothrixins 1, 2, and 15b-p and quinocarbazole analogues were investigated against nine cancer cell lines. The quinocarbazoles 21a and 25a inhibited the catalytic activity of human topoisomerase II. The plasmid DNA cleavage abilities of calothrixins 1, 2, and 15b-p identified compound 15h causing DNA cleavage comparable to that of calothrixin A (1). Calothrixin A (1), 3-fluorocalothrixin 15h and 4-fluoroquinocarbazole 21b induced extensive DNA damage followed by apoptotic cell death. Spectral and plasmid unwinding studies demonstrated an intercalative mode of binding for quinocarbazoles. We identified two promising drug candidates, the 3-fluorocalothrixin B 15h with low toxicity in animal model and its deoxygenated derivative 4-fluoroquinocarbazole 21b as having potent cytotoxicity against NCI-H460 cell line with a GI₅₀ of 1 nM.

Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking

The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.

Novel poly(ADP-ribose) polymerase inhibitor veliparib: biophysical studies on its binding to calf thymus DNA

Veliparib, an new anticancer drug in the class of poly (ADP-ribose) polymerase inhibitors, intercalates partially and binds to ctDNA and induces moderate conformational perturbation of the DNA.

Interaction of Catechu Dye with DNA: Spectroscopic and In Silico Approach

Catechin, a yellow colored molecule obtained from the wood of Acacia catechu was analyzed for its interaction with synthetic DNA duplexes using spectroscopic analysis. UV-Visible spectroscopic analysis revealed the non-intercalative binding mode. Fourier Transform Infrared spectroscopy (FTIR) analysis expose chemical shift indicated by various vibrational stretches and an increase in the intensity of base stacking was observed by Circular Dichroism (CD), respectively. This inference was further confirmed through nuclear staining technique and also in electrophoretic technique; the dye quenches the fluorescent intensity of ethidium bromide. The result of fluorescence spectroscopy was in concordance with the electrophoretic technique. In addition, the spectroscopic results were in accordance with the molecular docking studies of specific catechin compound from the catechu dye with CT-DNA. This kind of site specificity is a gain in the medicinal field as the drug can be DNA targeted for cancer therapeutics. The present work reveals that catechu dye has a noteworthy application in the field of medical bioscience.

Dihydroxyanthraquinone derivatives: natural dyes as blue-light-sensitive versatile photoinitiators of photopolymerization

Dihydroxyanthraquinone derivatives can be used as versatile blue-light-sensitive photoinitiators for cross-linked free radical photopolymerization, RAFT photopolymerization, and cationic photopolymerization.

Studies on interaction of norbixin with DNA: multispectroscopic and in silico analysis

The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08×10(5) Mol(-1) L. FTIR and CD studies were coupled with (1)H NMR spectra revealed that norbixin intercalates partially and binds to the groove's, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic.

Biophysical characterization and molecular docking studies of imidazolium based polyelectrolytes-DNA complexes: role of hydrophobicity

Nonviral gene delivery vectors are acquiring greater attention in the field of gene therapy by replacing the biological viral vectors. DNA-cationic polymer complexes are one of the most promising systems to find application in gene therapy. Hence, a complete insight of their biophysical characterization and binding energy profile is important in understanding the mechanism involved in nonviral gene therapy. In this investigation, the interaction between calf thymus DNA (ctDNA) and imidazolium-based poly(ionic liquids) (PILs) also known as polyelectrolytes with three different alkyl side chains (ethyl, butyl, and hexyl) in physiological conditions using various spectroscopic experiments with constant DNA concentration and varying polyelectrolyte concentrations is reported. UV-visible absorption, fluorescence quenching studies, gel electrophoresis, circular dichroism (CD), and Fourier transform infrared spectroscopy (FTIR) have confirmed the binding of polyelectrolytes with DNA. UV-vis absorption measurements and fluorescence quenching revealed that the binding between DNA and the polyelectrolyte is dominated by electrostatic interactions. Additionally, CD and FTIR results indicated that the DNA retained its B-form with minor perturbation in the phosphate backbone without significant change in the conformation of its base pairs. Preference for alkyl side chains (K(PIL-Ethyl Br) < K(PIL-Butyl Br) < K(PIL-Hexyl Br)) toward efficient binding between the polyelectrolyte and DNA was inferred from the binding and quenching constants calculated from the absorption and emission spectra, respectively. Further, in silico molecular docking studies not only validated the observed binding trend but also provided insight into the binding mode of the polyelectrolyte-DNA complex.

Photo-physical behavior of some antitumor anthracycline in solvent media with different polarity

Absorption and emission spectra of three antitumour anthracyclines, with various substituent and stereoisomer groups, were studied in different solvents. The solute's photo-physical behavior strongly depends on solvent-solute interactions and solvent's nature. Solvatochromic method was used to investigate dipole moments of these materials in ground and excited states. Spectral variations were analyzed via means of linear solvation energy relationships concept, proposed by Kamlet and Taft. The results explain the nature of specific and non-specific solvent-solute interactions and functional groups' reorientation of studied anthracyclines in different media.

In vitro protection of biological macromolecules against oxidative stress and in vivo toxicity evaluation of Acacia nilotica (L.) and ethyl gallate in rats

BACKGROUND

Recently, enormous research has been focused on natural bioactive compounds possessing potential antioxidant and anticancer properties using cell lines and animal models. Acacia nilotica (L.) is widely distributed in Asia, Africa, Australia and Kenya. The plant is traditionally used to treat mouth, ear and bone cancer. However, reports on Acacia nilotica (L.) Wild. Ex. Delile subsp. indica (Benth.) Brenan regarding its toxicity profile is limited. Hence in this study, we investigated the antioxidant capacity and acute toxicity of ethyl gallate, a phenolic antioxidant present in the A. nilotica (L.) leaf extract.

METHODS

The antioxidant activity of ethyl gallate against Fenton's system (Fe3+/H2O2/ascorbic acid) generated oxidative damage to pBR322 DNA and BSA was investigated. We also studied the interaction of ethyl gallate to CT-DNA by wave scan and FTIR analysis. The amount of ethyl gallate present in the A. nilotica (L.) leaf extract was calculated using HPLC and represented in gram equivalence of ethyl gallate. The acute toxicity profile of ethyl gallate in the A. nilotica (L.) leaf extract was analyzed in albino Wistar rats. Measurement of liver and kidney function markers, total proteins and glucose were determined in the serum. Statistical analysis was done using statistical package for social sciences (SPSS) tool version 16.0.

RESULTS

Ethyl gallate was found to be effective at 100 μg/mL concentration by inhibiting the free radical mediated damage to BSA and pBR322 DNA. We also found that the interaction of ethyl gallate and A. nilotica (L.) leaf extract to CT-DNA occurs through intercalation. One gram of A. nilotica (L.) leaf extract was found to be equivalent to 20 mg of ethyl gallate through HPLC analysis. Based on the acute toxicity results, A. nilotica (L.) leaf extract and ethyl gallate as well was found to be non-toxic and safe.

CONCLUSIONS

Results revealed no mortality or abnormal biochemical changes in vivo and the protective effect of A. nilotica (L.) leaf extract and ethyl gallate on DNA and protein against oxidative stress in vitro. Hence, A. nilotica (L.) leaf extract or ethyl gallate could be used as potential antioxidants with safe therapeutic application in cancer chemotherapy.

DNA-binding studies and antitumor evaluation of novel water soluble organic pip and hpip analogs

Two new water-soluble pip and hpip analogs, 1 and 2 pip = 2-phenylimidazo[4,5-f][1, 10]phenanthroline; hpip = 2-(2-hydroxyphenyl)imidazo[4,5-f][1, 10]phenanthroline, have been synthesized and fully characterized by CHN analysis, MALDI-TOF MS, (1)H-NMR, IR (ATR), and UV-Vis methods. The DNA-binding behaviors of both compounds have been studied by viscosity measurements, spectroscopic methods, and gel electrophoresis studies, and potential for antitumor activity was evaluated by measuring their ability to inhibit DNA transcription. The results indicate that both compounds show some strong binding to DNA in a mixture of electrostatic and intercalative mode resulting in the intrinsic binding constants Kb of (4.0 ± 0.5) × 10(5) M(-1) and (7.5 ± 0.5) × 10(5) M(-1) for 1 and 2, respectively. These strong binding affinities for DNA are comparable for that seen for many transition metal-based intercalators. Comparatively, observed difference in the DNA-binding affinities of two complexes can be reasonably explained by the presence of an intra-molecular hydrogen-bonding between the ortho-phenolic group and the nitrogen atom of the imidazole ring. The extended co-planarity of 2 due to the intramolecular hydrogen bonding may lead to an enhancement of DNA binding affinity of 2. In addition, 2 can promote cleavage of pBR322 DNA upon irradiation, it inhibits DNA transcription and it is more cytotoxic at lower concentrations in comparison to 1, as revealed by the spectroscopic measurements.