Quantification of mirtazapine in tablets via DNA binding mechanism; development of a new HPLC method

Atypical antidepressant mirtazapine (MIR) is mostly prescribed for the management of major depressive disorder. The identification of MIR in pharmaceutical dosage forms was made possible by developing a novel, quick, sensitive high-performance liquid chromatography (HPLC) approach that was verified in accordance with ICH recommendations. In the first part of this study, HPLC investigations were optimized with regard to variables including pH, working column, mobile phase, temperature, and flow rate. The limit of detection (LOD) was 0.013 ppm, the limit of quantification (LOQ) was 0.044 ppm, and the linear range was computed as 0.5-15 ppm (R2 = 0.9998). The recovery investigation assessed the method's accuracy, which was shown to range between 98.82 and 100.97 %. In the second part, by using UV-vis spectroscopy, HPLC, thermal denaturation, and viscosity measurements, the mechanism of binding interaction of MIR with double-stranded fish sperm deoxyribonucleic acid (dsDNA) has been thoroughly studied. The DNA binding constants (Kb) were determined using UV-Vis absorption and HPLC methods. To investigate the interactions of MIR with dsDNA, molecular docking calculations and additionally, molecular dynamics simulations were performed. Results showed that MIR is located in the minor groove of dsDNA, and in addition to hydrogen bonding, electrostatic interaction is also formed between the aromatic ring of MIR and phosphate oxygen of dsDNA. Finally, a binding characterization study using MIR tablets was also conducted in order to assess the interaction mechanism of the DNA with the drug using the validated analytical procedure developed for the MIR molecule.

Ternary Cobalt (II)-Metformin-Glycine/Histidine/Proline Complexes: Multispectroscopic DNA, HSA, and BSA Interaction and Cytotoxicity Studies

The synthesized water-soluble ternary complexes [Co(met)(gly)(Cl)2] (1), [Co(met)(hist)(Cl)2] (2), and [Co(met)(pro)(Cl)2] (3), (met = metformin, gly = glycine, hist = histidine, and pro = proline) were evaluated using spectro-analytical techniques, and the stereochemistry of the complexes was determined to be octahedral. UV-Vis absorption, competitive DNA-binding experiments using ethidium bromide (EB) by fluorescence, fluorescence emission studies, viscosity studies, and gel electrophoresis techniques were all employed to explore the binding characteristics of the cobalt (II) complexes with CT-DNA and groove-binding mechanism established. The salt-dependent association of the complexes to CT-DNA was investigated using UV-Vis spectrophotometric analysis. The association of the cobalt (II) complexes with BSA and HSA was explored by utilizing UV-Vis absorption and fluorescence spectroscopy approaches. The findings show that the complexes exhibit adequate capacity to quench BSA and HSA fluorescence and that the binding response is mostly a static quenching mechanism. The cytotoxicity of the complexes has also been appraised with the human breast adenocarcinoma cell lines (MCF-7) and (MDA-MB-231) by utilizing the MTT assay. For each cell line, the IC50 values were computed. In both cell lines, all the complexes were active.

Insight into the binding interactions of fluorenone-pendent Schiff base with calf thymus DNA

A novel fluorenone appended Schiff base (L) has been synthesized and utilized for studying the binding interactions with Calf Thymus DNA (ct-DNA). The mechanism of binding with ct-DNA was explored by employing various spectroscopic techniques viz. UV-Vis absorption spectroscopy, fluorescence emission spectroscopy, gel-electrophoresis, circular dichroism (CD), melting studies, viscosity arrays and molecular modelling methodology. The interpretation of UV-vis absorbance spectra pointed to binding of L within minor groove of ct-DNA with the binding constant of K_b = 0.15 × 10⁴ M^-1. Dye-displacement studies with Rhodamine-B (RhB) and Ethylene Bromide (EB) in fluorescence spectroscopy verified the groove binding mode of interaction between L and ct-DNA. Melting studies, circular dichroism, and viscosity studies further elucidated the binding modes of L with ct-DNA. Thermodynamic variable measurements taken at various temperatures such as ΔG^⁰, ΔH^⁰, and ΔS^⁰ revealed that hydrophobic forces played a significant role in the binding process. The meticulous computational interaction demonstrated by molecular docking confirmed the minor groove binding of L with ct-DNA.

Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods

Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x10⁴M^-1 (UV-vis) and 5.75x10⁴M^-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.

Elucidation of the interaction of apocarotenoids with calf thymus DNA by biophysical techniques and in vitro study in MCF-7 cells to explore their potential in cancer therapy

Objectives

DNA is one of the targets of cancer-therapeutic small molecules. Cisplatin, a DNA intercalator, is one of the first-line drugs in the cancer chemo regimen which comes with health-compromising side effects during chemotherapy. The synergistic effect of natural molecules with cisplatin can help to potentiate its anti-cancer efficacy and decrease its negative effect on health. Here, we report the interaction of cisplatin with calf thymus-DNA (ct-DNA) in combination with natural molecules like apocarotenoids which are reported for their therapeutic properties.

Materials and Methods

The combinatorial effect of apocarotenoids on ct-DNA was explored through various biophysical techniques such as UV-Visible spectroscopy, circular dichroism studies, DNA melt curve analysis, viscosity measurements, and an in vitro study in MCF-7 cells by cell cycle analysis.

Results

UV-Visible spectroscopy studies suggest apocarotenoids and their combination shows a non-intercalative mode of binding. Circular dichroism analysis showed no major changes in DNA form during the interaction of DNA with apocarotenoids and their respective combinations with cisplatin, which is suggestive of the groove-binding mode of apocarotenoids. DNA melt curve analysis showed a decrease in the intensity of the fluorescence for apocarotenoids with cisplatin which indicates the possibility of DNA interaction through groove binding. Viscosity studies suggested a groove binding mode of interaction of ct-DNA with apocarotenoids and their combination as there was minimal change in the viscosity measurements. The in vitro analysis exhibits that the apocarotenoids and their combination have a considerable effect on DNA synthesis.

Conclusion

This study provides a better perspective on the possible mode of interaction between ct-DNA and natural molecules along with cisplatin.

Nickel-Metformin Ternary Complexes: Geometrical, Thermal, DNA Binding, and Molecular Docking Studies

Novel three nickel(II) complexes of type [Ni(metf)(o-phen)₂]Cl₂ (1), [Ni(metf)(opda)₂]Cl₂ (2), [Ni(metf)(2-2'bipy)₂]Cl₂ (3), (Metf = metformin, o-phen = ortho-phenanthroline, opda = ortho-phenylenediamine, 2-2' bipy = 2-2' bipyridyl) were synthesized and characterized by various analytical and spectral techniques. Based on these studies, octahedral geometry is assigned to these complexes. The DNA binding properties of these complexes were investigated by absorption, emission, and viscosity studies. From the spectral data, it was concluded that the complexes bind to DNA through groove mode of binding. The intrinsic binding constants (K_b) from absorption spectroscopy were 1.60 × 10⁴, 3.57 × 10⁴, and 5.70 × 10⁴ M^-1 for 1, 2, and 3, respectively, and Stern-Volmer quenching constants (K_sv) from emission spectroscopy were 0.11, 0.87, and 0.24, respectively. Thermal degradation pattern of the compounds was studied and Coats-Redfern method is used to determine kinetic parameters for complexes 1, 2, and 3 from thermal studies. The software Discovery Studio 2.1 was used to assess the binding affinity and interaction pattern of complexes with the B-DNA receptor protein and complex 1 has the highest dock score.

Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA

The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in ¹H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.

Molecular rec§ognition of telomere DNA sequence by 2, 6 anthraquinone derivatives leads to thermal stabilization and induces apoptosis in cancer cells

According to current research, anti-cancer anthraquinones impact telomere disruption and may interact with G-quadruplex DNA that triggers signaling to apoptosis. The present study represents the biophysical investigation of oxidative stress, late apoptosis, and induced senescence among cancer cells after binding laboratory synthesized piperidine-based anthraquinone derivatives, 2, 6- Bis [(3-piperidino)acetamido)]anthracene-9,10-dione (N1P) and 2, 6-Bis [piperidino)propionamido]anthracene-9,10-dione (N2P), with G-quadruplex DNA. We employed biophysical approaches to explore the interaction of synthetic anthraquinone derivatives with quadruplex DNA sequences to influence biological activities in the presence of K⁺ and Na⁺ cations. The binding affinity for N2P and N1P are K_b = 5.8 × 10⁶ M^-1 and K_b = 1.0 × 10⁶ M^-1, respectively, leading to hypo-/hyper-chromism with 5-7 nm red shift and significant fluorescence quenching and changes in ellipticity resulting in external binding of both the ligands to G-quadruplex DNA. Ligand binding induced enhancement of thermostability of G4 DNA is greater in Na⁺ environment (ΔT_m = 34 °C) as compared to that in K⁺ environment (ΔT_m = 21 °C), thereby restricting telomerase binding access to telomeres. Microscopic images of treated cells indicated cellular shape, nuclear condensation, and fragmentation alterations. The findings pave the path for therapeutic research, given the great potential of modifying anthraquinone substituent groups towards improved efficacy, ROS generation, and G-quadruplex DNA selectivity.

Functional group substitutions influence the binding of benzophenone-type UV filters with DNA

As a class of possible carcinogens, benzophenone-type UV filters (BPs) widely exist in natural environments and organisms. The crucial step of the carcinogenic process induced by cancerous toxins is binding with DNA to form adducts. Here, the binding of 10 typical BPs, i.e., benzophenone (BP1), 2-hydroxyl benzophenone (BP2), 4-hydroxyl benzophenone (BP3), 2,2'-dihydroxyl benzophenone (BP4), 2,4-dihydroxyl benzophenone (BP5), 4,4'-dihydroxyl benzophenone (BP6), 2,4,4'-trihydroxyl benzophenone (BP7), 2,2',4,4'-tetrahydroxyl benzophenone (BP8), 2-hydroxyl-4-methoxyl benzophenone (BP9), and 2,2'-dihydroxyl-4-methoxyl benzophenone (BP10), with DNA was tested via fluorescence quenching experiments. Only hydroxyl group-substituted BPs could bind to DNA by groove binding mode, and the quenching constants were 0.93 × 10³-5.89 × 10³ L/mol. Substituted BPs were preferentially bound to thymine. Circular dichroism analysis confirmed that BPs could affect DNA base stacking but could not transform its B-form. Based on molecular electrostatic surface potential analyses, molecular dynamics simulations, and energy decomposition calculations, it could be found that the site and number of hydroxyl substitution changed the molecular polarity of BPs, thereby affecting the number and strength of hydrogen bonds between BPs and DNA. The hydroxyl substitution at site 2 was more conducive to binding than at site 4. This study is beneficial in comprehending the carcinogenic mechanisms of BPs.

A study of structure-activity relationship and anion-controlled quinolinyl Ag(I) complexes as antimicrobial and antioxidant agents as well as their interaction with macromolecules

In this communication, we feature the synthesis and in-depth characterization of a series of silver(I) complexes obtained from the complexation of quinolin-4-yl Schiff base ligands ((E)-2-((quinolin-4-ylmethylene)amino)phenol L_a, 2-(quinolin-4-yl)benzo[d]thiazole L_b, (E)-N-(2-fluorophenyl)-1-(quinolin-4-yl)methanimine L_c, (E)-N-(4-chlorophenyl)-1-(quinolin-4-yl)methanimine L_d, (E)-1-(quinolin-4-yl)-N-(p-tolyl)methanimine L_e, (E)-1-(quinolin-4-yl)-N-(thiophen-2-ylmethyl)methanimine L_f) and three different silver(I) anions (nitrate, perchlorate and triflate). Structurally, the complexes adopted different coordination geometries, which included distorted linear or distorted tetrahedral geometry. The complexes were evaluated in vitro for their potential antibacterial and antioxidant activities. In addition, their interactions with calf thymus-DNA (CT-DNA) and bovine serum albumin (BSA) were evaluated. All the complexes had a wide spectrum of effective antibacterial activity against gram-positive and gram-negative bacterial and good antioxidant properties. The interactions of the complexes with CT-DNA and BSA were observed to occur either through intercalation or through a minor groove binder, while the interaction of the complexes with BSA reveals that some of the complexes can strongly quench the fluorescence of BSA through the static mechanism. The molecular docking studies of the complexes were also done to further elucidate the modes of interaction with CT-DNA and BSA.

Metformin-Derived Water-Soluble Cobalt Complexes: Thermal, Spectroscopic, DNA Interaction, and Molecular Docking Studies

Novel three water-soluble cobalt (II) complexes of type [Co(metf)(o-phen)₂]Cl₂ (1), [Co(metf)(opda)₂]Cl₂ (2), and [Co(metf)(2-2'bipy)₂]Cl₂ (3) (Metf, metformin; o-phen, ortho-phenanthroline; opda, ortho-phenylenediamine; 2,2'-bipy, 2,2'-bipyridine) were synthesized and characterized by various analytical and spectral techniques. Based on these studies, octahedral geometry is assigned to these complexes. The stability of the complexes has been calculated from quantum chemical parameters using HOMO-LUMO energies. Thermal degradation pattern of the compounds was studied and Coats-Redfern method is used to determine kinetic parameters for complexes 1, 2, and 3 from thermal studies. The DNA interaction of these complexes was investigated by absorption, emission, and viscosity studies. From the spectral data, it was concluded that the complexes bind to DNA through groove mode of binding. The intrinsic binding constants (K_b) from absorption spectroscopy were 2.49 × 10⁴, 2.48 × 10⁴, and 2.64 × 10⁴ M^-1 for 1, 2, and 3, respectively, and Stern-Volmer quenching constants (K_sv) from emission spectroscopy were 0.21, 0.20, and 0.13, respectively. These complexes were screened for nuclease activity of pUC19 DNA, in the presence of H₂O₂. Discovery studio 2.1 software was used to evaluate binding affinity and interaction pattern of complexes with B-DNA receptor protein and the maximum dock score is seen for complex 2.

Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches

β-resorcylic acid (BR) is a phytochemical which is widely used in the food industry as a flavouring agent and preservative. It has also been found to exhibit antibacterial action against several types of food-borne bacteria. DNA is the main molecular target for many small molecules of therapeutic importance. Hence, the interest is rapidly growing among the researchers to elucidate the interaction between small molecules and DNA. Thus, paving the way to design novel DNA-specific drugs. In this study, an attempt was made to examine the mechanism of binding of BR with calf thymus DNA (ctDNA) with the help of various experiments based on spectroscopy and in silico studies. The spectroscopic studies like UV absorption and fluorescence affirmed the complex formation between BR and ctDNA. The observed binding constant was in the order of 10³ M^-1 which is indicative of the groove binding mechanism. These findings were further verified by dye-displacement assay, potassium iodide quenching, urea denaturation assay, the study of the effect of ssDNA, circular dichroism and DNA thermal denaturing studies. Different temperature-based fluorescence and isothermal titration calorimetry (ITC) experiments were employed to evaluate thermodynamic parameters. The analysis of thermodynamic parameters supports the enthalpically driven, exothermic and spontaneous nature of the reaction between BR and ctDNA. The forces involved in the binding process were mainly found to be hydrogen bonding, van der Waals and hydrophobic interactions. The results obtained from the molecular docking and molecular dynamics (MD) simulation were consistent with the in vitro experiments, which support the groove binding mode of BR with ctDNA.

Description of the calf thymus DNA-malathion complex behavior by multi-spectroscopic and molecular modeling techniques: EMF at low and high frequency approaches

OBJECTIVES

Small molecules can bind to DNA via covalent or non-covalent interactions, which results in altering or inhibiting the function of DNA. Thus, understanding the interaction patterns of medicines or other small molecules can be very crucial. In this study, the interaction between malathion and calf thymus DNA (ctDNA), in the absence and presence of electromagnetic field (EMF) at low and high frequencies, was investigated through various spectroscopies and viscosity measurements.

MATERIALS AND METHODS

The interaction studies were performed by means of absorbance, circular dichroism, fluorescence spectroscopy, viscosity, thermal melting, and molecular modeling techniques.

RESULTS

The fluorescence intensity of the ctDNA-malathion complex in the presence of EMF, has revealed quenching of fluorescence emission curves. The dynamic interaction and RLS studies have implied the changes in ctDNA-malathion complex throughout the presence of EMF which suggested that hydrophobic forces play the main role in the binding. Studies have revealed that malathion does not have any effect on binding ethidium bromide to ctDNA, which signifies the groove binding. The viscosity of ctDNA increased as the malathion concentration was enlarged. The circular dichroism technique suggested that the ellipticity values of the ctDNA-malathion complex have not increased with enhancing the malathion concentration. Molecular docking and dynamics studies have indicated a potent electrostatic interaction between ctDNA and malathion in the groove binding site.

CONCLUSION

The results of spectroscopic studies reinforced a potent interaction between malathion and ctDNA in the absence and presence of EMF which can help us for further pharmaceutical drug discoveries.

Change of benzo(a)pyrene during frying and its groove binding to calf thymus DNA

Benzo[a]pyrene (BaP), a prototype of polycyclic aromatic hydrocarbons (PAHs) with potential mutagenicity, toxicity and carcinogenicity, is ubiquitous in deep-fried foods. Herein, the changes in eight specific PAHs (PAH8) concentration in sunflower oil during frying were investigated by gas chromatography-triple quadrupole-mass spectrometry (GC-QqQ-MS). PAH8 concentrations in sunflower oil were 23.92-27.82 μg kg^-1 and increased with increasing frying time. The detected BaP levels were 3.64-4.00 μg kg^-1, exceeding the upper limit (2 μg kg^-1) set by European Union (EU), though below the limiting value (10 μg kg^-1) in China. The interaction between BaP and calf thymus DNA (ctDNA) was explored through various spectroscopic methods and molecular docking. Melting studies, denaturation experiments, ionic strength effects and viscosity measurements indicated that BaP interacted with ctDNA primarily via groove binding as evidenced by circular dichroism analysis and molecular docking. Further gel electrophoresis assays suggested that DNA was damaged at high levels of BaP.

Influence of position of hydroxyl group of flavonoids on their binding with single stranded polyriboadenylic acid: A spectroscopic evaluation

Single stranded polyriboadenylic acid [poly (rA)] has been accepted widely as a suitable drug target owing to its vital role in the development of cancer since it controls gene expression during cell growth and differentiation. The biological properties of poly (rA) depend on its structural morphology. Pharmacologically active flavonoids can act as suitable binders to poly (rA) and significantly change its biophysical properties. Different factors favour flavonoid-poly (rA) binding. In our present work we have explored the role played by the position of hydroxyl groups in the flavonoids namely 3, 5, 6 and 7 hydroxyflavones in their course of interaction with poly (rA). A range of spectroscopic experiments reveal that 3HF binds best to poly (rA) among the four chosen flavonoids. This is probably due to the presence of a hydroxyl group in '3' position that enables it to exhibit ESIPT phenomenon which is missing for the other used flavonoids.

Cytotoxicity and DNA interaction in a series of aryl terminated iminopyridine Pt(II) complexes

A series of iminopyridine complexes of platinum(II), bearing a flexible diethereal, aryl terminated residue, where the size of aryl group is varied from phenyl to 9-anthracenyl, was synthesized. The new complexes are soluble and stable in DMSO/H₂O mixtures. Besides the metal center, aryl groups are available for further interactions with DNA, due to the good side chain flexibility. The new aryl functionalized iminopyridine dichlorido platinum(II) complexes show a significant antiproliferative activity on ovarian carcinoma cells and notably, complex 13 is able to overcome cisplatin resistance. The study of the interaction mode of 13 with DNA highlighted the ability to form a molecular complex characterized by a dual (intercalative and groove binding) geometry. The complex is also able to covalently add to DNA even though interstrand cross-links appear significantly hampered with respect to cisplatin. The interactions with the macromolecule are discussed in view of the observed cell effect.

The interaction of light-activatable 2-thioxanthone thioacetic acid with ct-DNA and its cytotoxic activity: Novel theranostic agent

In this study, a thioxanthone derivative, 2-Thioxanthone Thioacetic Acid (TXSCH₂COOH) was used to analyze the type of binding to calf thymus DNA in a physiological buffer (Tris-HCl buffer solution, pH:7.0). Several spectroscopic techniques were employed including UV-Vis absorption and fluorescence emission spectroscopy and viscosity measurements were also used to clarify the binding mode of TXSCH₂COOH to ct-DNA. The intrinsic binding constant Kb of TXSCH₂COOH-ct-DNA was found as 2.5 × 10³ M^-1 from the absorption studies. Increasing of fluorescence emission intensity was found approximately 74.4% by adding ct-DNA to the TXSCH₂COOH solution. Fluorescence microscopy was employed to display imaging of the TXSCH₂COOH-ct-DNA solution. Increasing of the iodide quenching effect was observed when TXSCH₂COOH was added to the double stranded DNA and the calculated quenching constants of TXSCH₂COOH and TXSCH₂COOH-ct-DNA were found to be 1.89 × 10³ M^-1 and 1.19 × 10⁴ M^-1, respectively. Additionally, the iodide quenching experiment was conducted with single stranded DNA which led to a high Ksv value. All the experimental results including the viscosity values of ct-DNA with TXSCH₂COOH demonstrated that the binding of TXSCH₂COOH to ct-DNA was most likely groove binding. Furthermore, TXSCH₂COOH was found to be an A-T rich minor groove binder. This was confirmed by the displacement assays with Hoechst 33258 compared to Ethidium Bromide. The in vitro cytotoxic activity measurements were performed by MTT assay on HT29 cell line for 72 h. TXSCH₂COOH exhibited notable cytotoxic activities compared to the standard chemotherapy drugs, fluorouracil (5-FU), cisplatin in tumorigenic HT29 cell line. The 50% growth-inhibitory concentration (IC₅₀) for TXSCH₂COOH was 19,8 μg/mL while 5-FU and cisplatin were 28.9 μg/mL, 20 μg/mL, respectively. The increase in cytotoxic effect when TXSCH₂COOH is activated by light indicates the potential of being theranostic cancer drug candidate.

In vitro biological evaluation and consideration about structure-activity relationship of silver(I) aminoacidate complexes

Two silver(I) aminoacidate complexes {[Ag₄(L-HAla)₄(NO₃)₃]NO₃}_n (AgAla, complex 1, Ala = alanine) and {[Ag(L-Phe)]}_n (AgPhe, complex 2, Phe = phenylalanine) were prepared and characterized by elemental, spectral analysis (FT-IR, NMR techniques) and single crystal X-ray analysis in solid state and their solution stability was measured in biological testing time-scale by ¹H NMR. The bridging coordination modes of the zwitterionic Ala and deprotonated Phe ligands led to the formation of 1D polymeric chains of the complexes. The significant argentophilic interactions are presented in the structure of AgAla. Antimicrobial testing of prepared Ag(I) complexes was evaluated by IC₅₀ and MIC values and were compared with AgGly, silver(I) sulfadiazine and AgNO₃ samples. Moreover, MTS test was used to the testing of broad range antiproliferative activity of studied compounds against different cancer cell lines and also to the investigation of calf thymus DNA interactions by absorption spectroscopy, fluorescence spectroscopy, Ethidium bromide/Hoechst 33258 displacement experiments and circular dichroism spectroscopy. To evaluate the pUC19 DNA fragmentation by silver(I) complexes, the agarose gel electrophoresis was used. In addition to biological evaluation we used lipophilicity measurement results in the discussion about structure-activity relationship (SAR).

Multi-spectroscopic, voltammetric and molecular docking studies on binding of anti-diabetic drug rosigiltazone with DNA

The binding of an anti-diabetic drug rosiglitazone (RG) with calf-thymus DNA (CT-DNA) in physiological buffer (pH 7.4) has been investigated using various spectral techniques such as UV-Vis, fluorescence, ¹H NMR and circular dichroism (CD) coupled with viscosity measurement and molecular docking studies. The binding of RG with CT-DNA results in small hypochromism without any change in absorption maximum and fluorescence quenching with hardly any shifts in emission maximum suggesting groove binding mode of interaction. The binding constant is found to be 4.2 × 10² M^-1 at 298 K. Thermodynamic analysis reveal that the binding is spontaneous and H-bonding and van der Waals forces play predominant role in the binding of RG with CT-DNA. Competitive interaction between RG and ethidium bromide with CT-DNA, viscosity measurements, KI quenching, ¹H NMR and CD studies substantiate the prosed mode of binding. Voltammetric investigations suggest that the electro-reduction of RG is an adsorption controlled process and shift of reduction peak to more negative potential, with a binding constant of 3.4 × 10³ M^-1, validates the groove binding mode of interaction between RG and CT-DNA. Molecular docking reveals that RG binds in the minor groove of DNA and the dominating interaction forces are H-bonding and hydrophobic interactions.

PEP-FOLD design, synthesis, and characteristics of finger-like polypeptides

Polypeptides with finger-like structures can often intercalate into the grooves of DNA, thereby affecting DNA repair or activating gene transcription, both of which are crucial for the regulation of physiological processes. Their conserved amino acid sequence and simple structure have provided useful elements for the design and assembly of functional molecules. In this paper, using the C₂H₂ zinc finger domain and the PEP-FOLD3 online simulation platform 11 polypeptides containing 22 amino acid residues were designed. In addition, the CD spectroscopy was combined with the fluorescence spectroscopy to study the polypeptide structures and their interaction with DNA. Results showed that although addition of zinc ions affected the polypeptide structure, particularly of the polypeptides A4, B1, and B3, zinc ion was not an essential factor for increasing polypeptide-DNA interactions. Our study revealed an increase in the interaction strength between mutated polypeptides and DNA, suggesting that mutations disrupt polypeptide structure, and polypeptides interact with DNA by groove and electrostatic binding. Mutations at the 12th and 15th amino acid residues had the greatest effect. The stronger binding between A2 or B2 and DNA indicates that the polypeptide has a spatial structure that can stably interact with DNA. The structure and characteristics of these polypeptide domains can provide information for the design and development of new polypeptide functional molecules, which could have potential significance and applications. However, this information also suggests that there are many challenges facing polypeptide design due to the synergistic effects between the side chains of amino acid residues.

Synthesis, characterization, anti-proliferative properties and DNA binding of benzochromene derivatives: Increased Bax/Bcl-2 ratio and caspase-dependent apoptosis in colorectal cancer cell line

3-Amino-1-aryl-1H-benzo[f]chromene-2-carbonitrile derivatives were synthesized from three-component reaction of arylaldehyde, malononitrile and 2-naphthol in the presence of 1, 4-bis(4-ferrocenylbutyl)piperazine as a new catalyst. Cytotoxic potencies of the compounds were tested on HT-29 cells. 3-Amino-1-(4-fluorophenyl)-1H-benzo[f]chromene-2-carbonitrile (4c) was more active among these compounds and was selected for further studies. Apoptosis was investigated by acridine orange/ethidium bromide (AO/EtBr) double staining and flow cytometry. The qRT-PCR was used to analyze the expression of pro- and anti-apoptotic genes. The binding attributes of 4c with calf thymus DNA (ctDNA) was examined using multi-spectroscopic measurements. We found that 4c had potent cytotoxic activity against HT-29 cells with an IC₅₀ value of 60 µM through induction of cell cycle arrest in the sub-G1 phase and apoptosis. RT-PCR analysis demonstrated down-regulation of Bcl-2 expression, while the expression of Bax, caspase-3, -8 and -9 genes was up-regulated in HT-29 cells incubated with 4c compared with control cells. These studies revealed that 4c interacts with DNA through groove binding mode with the intrinsic binding constant (K_b) of 3 × 10² M^-1. Thus, 4c is a valuable candidate for further evaluation as a new series of potent chemotherapeutic family in colon cancer treatment.

Studies on the interaction of antibiotic drug rifampin with DNA and influence of bivalent metal ions on binding affinity

In this paper, the interaction between rifampin, a known antibiotic used against tuberculosis, and DNA helix is investigated by applying multiple biophysical and molecular modelling approaches in an aqueous solution at pH 7.4 and 5. It was proved that the fluorescence quenching of labeled probe DNA by rifampin is a result of the complex formation of rifampin in groove of DNA. Binding parameters were calculated using the logarithmic Hill equation to provide a quantitative term of the binding affinity between rifampin and DNA sites. The resulting ΔH⁰ = -122.76 ± 0.07 kJ/mol and ΔS⁰ = -308.19 ± 238.78 J/mol K confirms the role of the Van der Waals' forces and hydrogen bonding in the rifampin-DNA complexation. Furthermore, the influence of bivalent metal ions on the binding affinity was resulted in order of Cu(II) > Ca(II) > Co(II) > Zn(II).

DNA minor groove binding of a well known anti-mycobacterial drug dapsone: A spectroscopic, viscometric and molecular docking study

Dapsone is a sulfone drug mainly used as anti-microbial and anti-inflammatory agent for the treatment of various diseases including leprosy. Recently, its interaction with protein (bovine serum albumin) is evidenced. But, the binding propensity of this anti-mycobacterial drug towards DNA is still unknown. Also, the mode of dapsone-DNA interaction (if any) is still an unknown quantity. In this study, we have taken a thorough attempt to understand these two unknown aspects using various biophysical and in silico molecular docking techniques. Both UV-visible and fluorescence titrimetric studies indicated that dapsone binds to CT-DNA with a binding constant in order of 10⁴ M^-1. Circular dichroism, thermal denaturation and viscosity experiments revealed that dapsone binds to the grooves of CT-DNA. Competitive DNA binding studies clearly indicated the minor groove binding property of this anti-mycobacterial drug. Molecular docking provided detailed information about the formation of hydrogen bonding in the dapsone-DNA complex. This in silico study further revealed that dapsone binds to the AT-rich region of the minor groove of DNA having a relative binding energy of -6.22 kcal mol^-1. Overall, all these findings evolved from this study can be used for better understanding the medicinal importance of dapsone.

Photophysical and thermodynamic evaluation on the in vitro and in silico binding profile of Camptothecin with DNA

Camptothecin (CMT) is an anti-tumour alkaloid drug exhibiting selective topoisomerase-I inhibitory activity by eventually hindering dynamic functions of DNA duplex via initiating apoptosis. Unravelling the binding mechanism of CMT with bio macromolecular systems can offer fundamental information regarding the mechanism of actions which can lead to the design of rational proactive drugs. This study endeavoured the binding interactions of CMT with calf thymus DNA (ct-DNA) along with the structural alterations attained by the DNA duplex owing to CMT interactions through multi-spectroscopic, calorimetric and molecular docking studies. The UV-visible absorbance and fluorescence quenching studies revealed the binding strength of CMT with ct-DNA, evident from the binding constants K₁ = 3.79 × 10³ M^-1 and Kq = 2 × 10³ M^-1. The time-resolved lifetime measurements inferred that the quenching was static due to the non-fluorescent ground state complex formation. The dye displacement study, temperature melting and viscosity measurements established a typical non-intercalative binding mode of CMT with ct-DNA. The binding isotherm deduced from ITC was found to be spontaneous and exothermic exerting a promising ΔG value of -6.2 kcal mol^-1. The thermal kinetic parameters implied that the forces primarily involved in the CMT-ct-DNA complexation are hydrogen bonding and van der Waals interactions. Moreover, the structural alterations of DNA duplex reflected in the CD and FTIR spectra could undeniably confirm the groove binding manner of CMT. The in silico extra precision docking study explored more accurate molecular illustrations of sequence specific minor groove binding mechanism evolved between CMT and DNA corroborating well with the experimental results. These innovative findings may shorten the path towards the development of novel and more effective CMT drug derivatives.

DNA binding, prominent photonuclease activity and antibacterial PDT of cobalt(II) complexes of phenanthroline based photosensitizers

The chemistry of Co(II) complexes showing efficient light induced DNA cleavage activity, binding propensity to calf thymus DNA and antibacterial PDT is summarized in this article. Complexes of formulation [Co(mqt)(B)₂]ClO₄ 1-3 where mqt is 4-methylquinoline-2-thiol and B is N,N-donor heterocyclic base, viz. 1,10-phenanthroline (phen 1), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq 2) and dipyrido[3,2-a:2',3'-c]phenazine (dppz 3) have been prepared and characterized. The DNA-binding behaviors of these three complexes were explored by absorption spectra, viscosity measurements and thermal denaturation studies. The DNA binding constants for complexes 1, 2 and 3 were determined to be 1.6 × 10³ M^-1, 1.1 × 10⁴ M^-1 and 6.4 × 10⁴ M^-1 respectively. The experimental results suggest that these complexes interact with DNA through groove binding mode. The complexes show significant photocleavage of supercoiled (SC) DNA proceeds via a type-II process forming singlet oxygen as the reactive species. Antimicrobial photodynamic therapy was studied using photodynamic antimicrobial chemotherapy (PACT) assay against E. coli and all complexes exhibited significant reduction in bacterial growth on photoirradiation.

Spectrophotometric study on binding of 2-thioxanthone acetic acid with ct-DNA

Thioxanthone and its derivatives are the most remarkable molecules due to their vast variety of application such as radiation curing that is, until using them as a therapeutic drug. Therefore, in this study it was intended to use 2-Thioxanthone acetic acid with and without NaCl in Tris HCl buffer solution (pH:7.0) to represent the interaction with ct-DNA. The UV-vis absorption spectra of TXCH₂COOH in the presence of ct-DNA showed hypochromism and the intrinstic binding constant (K_b) was determined as 6 × 10³ L mol^-1. The fluoresence intensity of TXCH₂COOH with ct-DNA clearly increased up to 101% which indicated that the fluorescence intensity was very sensitive to ct-DNA concentration. The binding constant (K) and the values of number of binding sites (n) and were calculated as 1.8 × 10³ L mol^-1 and 0.69, respectively. When the quenching constants (K_sv) of free TXCH₂COOH and TXCH₂COOH, which were bonded with ct-DNA were compared, slightly changed values of Ksv were seen. Moreover, displacement assay with Hoechst 33,258 and viscosity measurements in the presence and absence of NaCl salt also confirmed the binding mode which noted the electrostatic interaction following groove binding between TXCH₂COOH and ct-DNA. Last but not least, the salt effect was examined on ct-DNA binding with TXCH₂COOH. The results of the experiments indicated that the groove binding was strengthened by NaCl whereas in the high NaCl concentration, the binding ability of TXCH₂COOH to ct-DNA was inversely affected.

Exploration of intermolecular interaction of calf thymus DNA with sulfosulfuron using multi-spectroscopic and molecular docking techniques

As a sulfonylurea herbicide, sulfosulfuron is extensively applied in controlling broad-leaves and weeds in agriculture. It may cause a potential risk for human and herbivores health due to its widely application and residue in crops and fruits. The study of the binding characteristics of calf thymus DNA (ct-DNA) with sulfosulfuron was performed through a series of spectroscopic techniques and computer simulation. The experimental results showed sulfosulfuron interacted with ct-DNA through the groove binding. The negative values of thermodynamic parameter (ΔH⁰, ΔS⁰ and ΔG⁰) revealed that the reaction of sulfosulfuron with DNA could proceed spontaneously, and the hydrogen bonding and van der Waals forces were essential to sulfosulfuron-ct-DNA binding, which was further verified by molecular docking study. Meanwhile, the electrostatic and hydrophobic interactions also played a supporting function for the interaction of sulfosulfuron with ct-DNA. The circular dichroism (CD) results exhibited a minor change in the secondary structure of ct-DNA during interaction process. Moreover, the conformation of sulfosulfuron had the obvious change after binding to DNA, which suggested that the flexibility of sulfosulfuron contributed to stabilizing the sulfosulfuron-ct-DNA complex.

Multispectroscopic and Computational Investigation of ct-DNA Binding Properties with Hydroxybenzylidene Containing Tetrahydrocarbazole Derivative

Mode of interaction of a new tetrahydrocarbazole derivative with ct-DNA has been investigated systematically using fluorescence spectroscopy, UV-Vis spectroscopy and circular dichroism spectroscopy. It is concluded that TAH could intercalate into the base pairs of ct-DNA, and the fluorescence quenching by ct-DNA was static quenching type. Beside the multispectroscopic results, computational studies were done. Molecular docking results revealed that the TAH-DNAs complexes might be classified as druggable molecule in drug design. Additionally, DNA binding studies exhibited that TAH complexes have different interaction and orientation abilities to each DNA isomer. Combination of experimental and computational data showed that reported TAH is promising structure and deserves further applications.

Copper-metformin ternary complexes: Thermal, photochemosensitivity and molecular docking studies

The copper(II) complexes [Cu(Cl)₂(met)(o-phen)] (1), [Cu(Cl)₂(met)(en)] (2) and [Cu(Cl)₂(met)(opda)] (3) (met = metformin, o-phen = ortho-phenanthroline, en = ethylenediamine, opda = ortho-phenylenediamine) were synthesized and characterized by LC-MS, elemental analysis, molar conductance, thermal analysis, infrared spectra, magnetic moment, electronic spectra and XRD studies. The metal center was found in an octahedral geometry. The activation thermodynamic properties were calculated using Coats-Redfern method. Thermal decomposition processes of complexes 1, 2, 3 are non-spontaneous, i.e., the complexes are thermally stable. The positive value of Gibbs free energy of decomposition (ΔG^⁎) for the Cu(II) complexes is non-spontaneous processes. UV-Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV-Vis spectrum with DNA. The binding constants K_b from UV-Vis absorption studies were 4.6 × 10⁵, 1.48 × 10⁵, 2.09 × 10⁵ M^-1 for 1, 2, 3 respectively and Stern-Volmer quenching constants (K_sq) from fluorescence studies were 0.636, 0.293, 0.487 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT-DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decreases in the order of 1 > 3 > 2. The complexes were docked in to B-DNA sequence, 5'(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3' retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.

Multi-spectroscopic and molecular docking studies on the interaction of darunavir, a HIV protease inhibitor with calf thymus DNA

Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV-ct-DNA complex having binding affinities of the order of 10³M^-1, which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (ΔH⁰) and entropy change (ΔS⁰) were -63.19kJ mol^-1 and -141.92J mol^-1K^-1, indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA.

Spectroscopic profiling and computational study of the binding of tschimgine: A natural monoterpene derivative, with calf thymus DNA

DNA is a major target for a number of anticancer substances. Interaction studies between small molecules and DNA are essential for rational drug designing to influence main biological processes and also introducing new probes for the assay of DNA. Tschimgine (TMG) is a monoterpene derivative with anticancer properties. In the present study we tried to elucidate the interaction of TMG with calf thymus DNA (CT-DNA) using different spectroscopic methods. UV-visible absorption spectrophotometry, fluorescence and circular dichroism (CD) spectroscopies as well as molecular docking study revealed formation of complex between TMG and CT-DNA. Binding constant (K_b) between TMG and DNA was 2.27×10⁴M^-1, that is comparable to groove binding agents. The fluorescence spectroscopic data revealed that the quenching mechanism of fluorescence of TMG by CT-DNA is static quenching. Thermodynamic parameters (ΔH<0 and ΔS<0) at different temperatures indicated that van der Waals forces and hydrogen bonds were involved in the binding process of TMG with CT-DNA. Competitive binding assay with methylene blue (MB) and Hoechst 33258 using fluorescence spectroscopy displayed that TMG possibly binds to the minor groove of CT-DNA. These observations were further confirmed by CD spectral analysis, viscosity measurements and molecular docking.

The effect of dimerization on the interaction of ibuprofen drug with calf thymus DNA: Molecularmodeling and spectroscopic investigation

The interaction between the dimer structure of ibuprofen drug (D-IB) and calf thymus DNA under simulative physiological conditions was investigated with the use of Hoechst 33258 and methylene blue dye as spectral probes by the methods of UV-visible absorption, fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling study.Using the Job's plot, a single class of binding sites for theD-IB on DNA was put in evidence. The Stern-Volmer analysis of fluorescence quenching data shows the presence of both the static and dynamic quenching mechanisms. The binding constants, K_b were calculated at different temperatures, and the thermodynamic parameters ∆G^∘, ∆H^∘ and ∆S^∘ were given. The experimental results showed that D-IB molecules could bind with DNA via groove binding mode as evidenced by: I. DNA binding constant from spectrophotometric studies of the interaction of D-IB with DNA is comparable to groove binding drugs. II. Competitive fluorimetric studies with Hoechst 33258 have shown that D-IB exhibits the ability of this complex to displace with DNA-bounded Hoechst, indicating that it binds to DNA in strong competition with Hoechst for the groove binding. III. There is no significantly change in the absorption of the MB-DNA system upon adding the D-IB, indicates that MB molecules are not released from the DNA helix after addition of the D-IB and are indicative of a non-intercalative mode of binding. IV. Small changes in DNA viscosity in the presence of D-IB, indicating weak link to DNA, which is consistent with DNA groove binding. As well as, induced CD spectral changes, and the docking results revealed that groove mechanism is followed by D-IB to bind with DNA.

Disquisition on the interaction of ibuprofen-Zn(II) complex with calf thymus DNA by spectroscopic techniques and the use of Hoechst 33258 and Methylene blue dyes as spectral probes

The interaction between ibuprofen-Zn(II) complex and calf thymus DNA in physiological buffer (pH 7.4) was studied with the use of Hoechst 33258 and methylene blue dyes as spectral probes by multi-spectroscopic techniques, and viscosity measurements. It was found that ibuprofen-Zn(II) complex molecules could bind with DNA via groove binding mode as evidenced by: i- DNA binding constant (K_b = (1.00 ± 0.2) × 10⁴ M^-1) from Spectrophotometric studies of the interaction of ibuprofen-Zn(II) complex with DNA is comparable to groove binding drugs. ii- Absorption Spectra of Competitive interaction of ibuprofen-Zn(II) complex and Hoechst 33258 with DNA exhibited the reverse process, The results suggested that interaction of the ibuprofen-Zn(II) complex with calf thymus DNA, is similar to Hoechst 33258 interaction with calf thymus DNA (This was verified by the following fluorescence study). iii- Competitive fluorimetric studies with Hoechst 33258 have shown that ibuprofen-Zn(II) complex exhibit the ability of this complex to displace with DNA-bounded Hoechst 33258, indicating that it binds to DNA in strong competition with Hoechst 33258 for the groove binding. iv- There is no significantly change in the fluorescence intensity of the MB-DNA system upon adding the ibuprofen-Zn(II) complex, indicate that MB molecules are not released from the DNA helix after addition of the ibuprofen-Zn(II) complex and are indicative of a non-intercalative mode of binding. v- Small changes in DNA viscosity in the presence of ibuprofen-Zn(II) complex, indicating weak link to DNA, which is consistent with DNA groove binding. As well as, induced CD spectral changes, and the docking results revealed that groove mechanism is followed by ibuprofen-Zn(II) complex to bind with DNA.

Role of hydroxyl groups in the B-ring of flavonoids in stabilization of the Hoogsteen paired third strand of Poly(U).Poly(A)*Poly(U) triplex

We have reported the interaction of two flavonoids namely quercetin (Q) and morin (M) with double stranded poly(A).poly(U) (herein after A.U) and triple stranded poly(U).poly(A)*poly(U) (herein after U.A*U, dot represents the Watson-Crick and asterisk represents Hoogsteen base pairing respectively) in this article. It has been observed that relative positions of hydroxyl groups on the B-ring of the flavonoids affect the stabilization of RNA. The double strand as well as the triple strand of RNA-polymers become more stabilized in presence of Q, however both the duplex and triplex remain unaffected in presence of M. The presence of catechol moiety on the B-ring of Q is supposed to be responsible for the stabilization. Moreover, after exploiting a series of biophysical experiments, it has been found that, triple helical RNA becomes more stabilized over its parent duplex in presence of Q. Fluorescence quenching, viscosity measurement and helix melting results establish the fact that Q binds with both forms of RNA through the mode of intercalation while M does not bind at all to either forms of RNA.

Insight into the binding of a non-toxic, self-assembling aromatic tripeptide with ct-DNA: Spectroscopic and viscositic studies

The report describes the synthesis, self-association and DNA binding studies of an aromatic tripeptide H-Phe-Phe-Phe-OH (FFF). The peptide backbone adopts β-sheet conformation both in solid and solution. In aqueous solution, FFF self-assembles to form nanostructured aggregates. Interactions of this peptide with calf-thymus DNA (ct-DNA) have been studied using various biophysical techniques including ultraviolet (UV) absorption spectroscopy, fluorescence spectroscopy and circular dichroism (CD) spectroscopy. The value of mean binding constant calculated from UV and fluorescence spectroscopic data is (2.914 ± 0.74) x 103 M-1 which is consistent with an external binding mode. Fluorescence intercalator displacement (FID) assay, iodide quenching study, viscosity measurement and thermal denaturation study of DNA further confirm the groove binding mode of peptide, FFF with ct-DNA. MTT cell survival assay reveals very low cytotoxicity of the peptide toward human lung carcinoma cell line A549.

Review on the binding of anticancer drug doxorubicin with DNA and tRNA: Structural models and antitumor activity

In this review, we have compared the results of multiple spectroscopic studies and molecular modeling of anticancer drug doxorubicin (DOX) bindings to DNA and tRNA. DOX was intercalated into DNA duplex, while tRNA binding is via major and minor grooves. DOX-DNA intercalation is close to A-7, C-5, *C-19 (H-bonding with DOX NH2 group), G-6, T-8 and T-18 with the free binding energy of -4.99kcal/mol. DOX-tRNA groove bindings are near A-29, A-31, A-38, C-25, C-27, C-28, *G-30 (H-bonding) and U-41 with the free binding energy of -4.44kcal/mol. Drug intercalation induced a partial B to A-DNA transition, while tRNA remained in A-family structure. The structural differences observed between DOX bindings to DNA and tRNA can be the main reasons for drug antitumor activity. The results of in vitro MTT assay on SKC01 colon carcinoma are consistent with the observed DNA structural changes. Future research should be focused on finding suitable nanocarriers for delivery of DOX in vivo in order to exploit the full capacity of this very important anticancer drug.

Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA

Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 10(4)Lmol(-1), and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.

Electrochemical, spectroscopic, and theoretical studies on the interaction between azathioprine and DNA

Possible interaction between immunosuppressive drug, azathioprine, and calf thymus DNA was explored by cyclic voltammetry, spectrophotometry, competitive spectrofluorimetry, circular dichroism spectroscopy (CD), and viscosity measurements. Cyclic voltammetry showed negative shift in the reduction peak of azathioprine in the presence of DNA, and large decrease in peak current, referring to the predominance of electrostatic forces. The binding constant was calculated to be 1.22×10(3)M(-1). Absorption hyperchromism without shift in wavelength was observed when DNA was added to azathioprine solution. Competitive fluorescence experiments were conducted by using Hoechst 33258 and methylene blue as probes for minor groove and intercalation binding modes, respectively. The studies showed that azathioprine could release Hoechst 33258, while negligible effect was detected in the case of methylene blue. Stern-Volmer quenching constant (KSV) and complex formation constant (Kf) were obtained from the fluorescence measurements to be 7.6×10(3)M(-1) and 7.76×10(4)M(-1), respectively, at 298K. Enthalpy and entropy changes during the interaction between azathioprine and DNA were calculated from Van't Hoff plot (ΔH=-20.2kJmol(-1); ΔS=26.11Jmol(-1)K(-1) at 298K) which showed an exothermic spontaneous reaction, and involvement of electrostatic forces in the complex formation with DNA. Moreover, circular dichroism studies revealed that azathioprine induced detectable changes in the negative band of DNA spectrum. Viscosity of DNA solution decreased in the presence of azathioprine, showed a non-intercalative mode of interaction. Finally, molecular docking calculations showed that in the lowest energy level of drug-DNA complex, azathioprine approaches the minor grooves of DNA.

Groove binding mediated structural modulation and DNA cleavage by quinoline appended chalcone derivative

The present study embodies the detail DNA binding interaction of a potential bioactive quinoline appended chalcone derivative (E)-3-(anthracen-10-yl)-1-(6,8-dibromo-2-methylquinolin-3-yl)prop-2-en-1-one (ADMQ) with calf thymus DNA (ctDNA) and its consequences by UV-Vis absorption, steady state fluorescence spectroscopy, fluorescence anisotropy, circular dichromism, helix melting, agarose gel electrophoresis, molecular docking, Induced Fit Docking (IFD) and molecular dynamics (MD) simulation. The UV-Vis absorption and fluorescence study reveal that the molecule undergoes considerable interaction with the nucleic acid. The control KI quenching experiment shows the lesser accessibility of ADMQ molecule to the ionic quencher (I(-)) in presence of ctDNA as compared to the bulk aqueous phase. Insignificant change in helix melting temperature as well as in circular dichromism (CD) spectra points toward non-covalent groove binding interaction. The moderate rotational confinement of this chalcone derivative (anisotropy=0.106) trapped in the nucleic acid environment, the comparative displacement assay with well-known minor groove binder Hoechst 33258 and intercalator Ethidium Bromide establishes the minor groove binding interactions of the probe molecule. Molecular docking, IFD and MD simulation reveal that the DNA undergoes prominent morphological changes in terms of helix unwinding and bending to accommodate ADMQ in a crescent shape at an angle of 110° in a sequence specific manner. During interaction, ADMQ rigidifies and bends the sugar phosphate backbone of the nucleic acid and thereby shortens its overall length by 3.02Å. Agarose gel electrophoresis experiment with plasmid pBR 322 reveals that the groove binded ADMQ result in a concentration dependent cleavage of plasmid DNA into its supercoiled and nicked circular form. The consolidated spectroscopic research described herein provides quantitative insight into the interaction of a heterocyclic chalcone derivative with relevant target nucleic acid, which may be useful for the future research on chalcone based therapeutic agents.

Racemic R,S-venlafaxine hydrochloride-DNA interaction: experimental and computational evidence

The interaction of racemic R,S-venlafaxine hydrochloride (rac-VEN) drug with calf thymus deoxyribonucleic acid (ct-DNA) was studied using various physico-chemical techniques and molecular docking at simulated physiological conditions (pH=7.4). The fluorescence study shows that ct-DNA interacted with rac-VEN and quenched its intrinsic fluorescence in a static quenching process. These results are further supported by UV-Vis spectra. The binding constant of rac-VEN with ct-DNA (0.57 × 10(4)) obtained from the spectroscopic techniques, which is more in keeping with the groove binding with DNA. Furthermore, the competition experiment using Hoechst33258 indicated that rac-VEN may bind to ct-DNA by a minor groove binding mode. In addition, iodide quenching effect on the fluorescence of rac-VEN before and after the interaction with ct-DNA is another evidence to groove binding. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the binding reaction. Molecular simulation studies carried out by using the AutoDock4 and Spartan 10 programs. From the best docking map, we found that R and S-isomers fit in the A6T7T8/T19A18A17 region in minor groove of B-DNA. Finally, these results indicated that the docking of S-VEN-B-DNA is more stable than R-VEN-B-DNA.

Studying non-covalent drug-DNA interactions

Drug-DNA interactions have been extensively studied in the recent past. Various techniques have been employed to decipher these interactions. DNA is a major target for a wide range of drugs that may specifically or non-specifically interact with DNA and affect its functions. Interaction between small molecules and DNA are of two types, covalent interactions and non-covalent interactions. Three major modes of non-covalent interactions are electrostatic interactions, groove binding and intercalative binding. This review primarily focuses on discussing various techniques used to study non-covalent interactions that occur between drugs and DNA. Additionally, we report several techniques that may be employed to analyse the binding mode of a drug with DNA. These techniques provide data that are reliable and simple to interpret.

Spectroscopic and computational studies on the interaction of DNA with pregabalin drug

The interaction of the drug pregabalin (S-3-(aminomethyl)-5-methylhexanoic acid) with CT-DNA was studied by using fluorescence spectroscopy, UV-Vis, CD, molecular docking study and viscometery. The fluorescence and UV absorption spectroscopy indicated that the drug interacted with CT-DNA in a groove binding mode. The binding constant and the number of binding sites were 5.6×10(4)Lmol(-1) and 0.96, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH=33.11kJmol(-1); ΔS=48.84Jmol(-1)K(-1)). Furthermore, the drug does not induce any changes in DNA viscosity. Circular dichroism spectroscopy (CD) was employed to measure the conformational changes of CT-DNA in the presence of the drug, which verified the groove binding mode. The molecular modeling results illustrated that the drug binds to groove of DNA by relative binding energy of docked structure -21.9kJmol(-1).

Spectroscopic and molecular docking studies on the interaction of the drug olanzapine with calf thymus DNA

The present study investigated the binding interaction between olanzapine and calf thymus DNA (ct-DNA) using emission, absorption, circular dichroism, viscosity measurements and molecular modeling. Thermodynamic parameters (ΔH<0 and ΔS<0) indicated that hydrogen bond and van der Waals play main roles in the binding of the drug to ct-DNA. Spectrophotometric studies of the interaction of olanzapine with DNA have shown that it could bind to ct-DNA (Kb=2×10(3)M(-1)). The binding constant is comparable to standard groove binding drugs. Competitive fluorimetric studies with Hoechst 33258 have shown that olanzapine exhibits the ability to displace the DNA-bound Hoechst 33258 indicating that binds strongly in minor groove of DNA helix. Furthermore, the drug induces detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity. All of the experimental results prove that the groove binding must be predominant. The results obtained from experimental data were in good agreement with molecular modeling studies.

Groove binding interaction between daphnetin and calf thymus DNA

The binding characteristics of daphnetin with calf thymus DNA (ctDNA) were investigated by multispectroscopic and chemometric approaches coupled with DNA viscosity measurements, melting studies and molecular docking technique. The expanded UV-vis spectral data matrix was processed by multivariate curve resolution-alternating least-squares method to obtain the concentration profiles of the components (daphnetin, ctDNA and daphnetin-ctDNA complex) to quantitatively monitor the daphnetin-ctDNA interaction. The groove mode of daphnetin binding to ctDNA was concluded by little change in melting temperature, viscosity of ctDNA and iodide quenching effect as well as increase in single-stranded DNA quenching effect. Moreover, the quantitative data for the competitive binding between daphnetin and Hoechst 33258 for ctDNA obtained by resolving the three-way synchronous fluorescence spectra data using parallel factor analysis modeling further supported the groove binding. The molecular docking visualized the results of the Fourier transform infrared analysis that the adenine and thymine bases in the minor groove of ctDNA were the main binding sites for daphnetin, and the circular dichroism spectra showed that the groove binding of daphnetin to ctDNA led to the conformational change in ctDNA from B-form to A-form. This study revealed the interaction mechanism of daphnetin with ctDNA.

In vitro studies on the behavior of salmeterol xinafoate and its interaction with calf thymus DNA by multi-spectroscopic techniques

The salmeterol xinafoate (SX) binding to calf thymus DNA in vitro was explored by fluorescence, resonance light scattering (RLS), UV-vis absorption, as well as viscometry, ionic strength effect and DNA melting techniques. It was found that SX could bind to DNA weakly, and the binding constants (Ka) were determined as 8.52×10(3), 8.31×10(3) and 6.14×10(3) L mol(-1) at 18, 28 and 38°C respectively. When bound to DNA, SX showed fluorescence quenching in the fluorescence spectra and hyperchromic effect in the absorption spectra. Stern-Volmer plots revealed that the quenching of fluorescence of SX by DNA was a static quenching. Furthermore, the relative viscosity and melting temperature of DNA solution were hardly influenced by SX, while the fluorescence intensity of SX-DNA was observed to decrease with the increasing ionic strength of system. Also, the binding constant between SX and double stranded DNA (dsDNA) was much weaker than that between SX and single stranded DNA (ssDNA). All these results suggested that the binding mode of SX to DNA should be groove binding. The obtained thermodynamic parameters indicated that electrostatic force might play a predominant role in SX binding to DNA. The quantum yield (φ) of SX was measured as 0.13 using comparative method. Based on the Förster resonance energy transfer theory (FRET), the binding distance (r0) between the acceptor and donor was calculated as 4.10 nm.

Proposed model for binding of permethrin and deltamethrin insecticides with ct-DNA, a structural comparative study

In this work, the interaction of two synthetic pyrethroid insecticides, permethrin (PER) and deltamethrin (DEL), with ct-DNA has been studied by cyclic voltammetry (CV), circular dichroism (CD), competitive fluorescence, atomic force microscopy (AFM), UV-vis spectroscopy, thermodynamic measurements, Fourier-transform infra-red (FT-IR), high performance liquid chromatography (HPLC) and two-layered ONIOM (our N-layered integrated molecular orbital+molecular mechanics) (DFT B3LYP, 6-31++G(d, p):UFF) molecular modeling methods. The last four methods were also utilized to study the binding of DEL with DNA. The results revealed that the PER may interact through partial intercalation and groove binding process while the PER only interacts through groove binding. Finally, the insecticides structure effect on interaction is discussed.

Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: advances toward treatment of hepatitis B virus infections

The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33±0.2×10(4) L mol(-1)and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH=34.4 kJ mol(-1); ΔS=184.32 J mol(-1) K(-1)). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol(-1). This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

Interaction of a copper (II) complex containing an artificial sweetener (aspartame) with calf thymus DNA

A copper (II) complex containing aspartame (APM) as ligand, Cu(APM)2Cl2⋅2H2O, was synthesized and characterized. In vitro binding interaction of this complex with native calf thymus DNA (CT-DNA) was studied at physiological pH. The interaction was studied using different methods: spectrophotometric, spectrofluorometric, competition experiment, circular dichroism (CD) and viscosimetric techniques. Hyperchromicity was observed in UV absorption band of Cu(APM)2Cl2⋅2H2O. A strong fluorescence quenching reaction of DNA to Cu(APM)2Cl2⋅2H2O was observed and the binding constants (Kf) and corresponding numbers of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy change (ΔH) and entropy change (ΔS) were calculated to be+89.3 kJ mol(-1) and+379.3 J mol(-1) K(-1) according to Van't Hoff equation which indicated that reaction is predominantly entropically driven. Experimental results from spectroscopic methods were comparable and further supported by viscosity measurements. We suggest that Cu(APM)2Cl2⋅2H2O interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 8×10+4 M(-1). Binding of this copper complex to DNA was found to be stronger compared to aspartame which was studied recently.