Study on the interaction of the drug mesalamine with calf thymus DNA using molecular docking and spectroscopic techniques

Elucidating the Interaction of Indole-3-Propionic Acid and Calf Thymus DNA: Multispectroscopic and Computational Modeling Approaches

Indole-3-propionic acid (IPA) is a plant growth regulator with good specificity and long action. IPA may be harmful to human health because of its accumulation in vegetables and fruits. Therefore, in this study, the properties of the interaction between calf thymus DNA (ctDNA) and IPA were systematically explored using multispectroscopic and computational modeling approaches. Analysis of fluorescence spectra showed that IPA binding to ctDNA to spontaneously form a complex was mainly driven by hydrogen bonds and hydrophobic interaction. DNA melting analysis, viscosity analysis, DNA cleavage study, and circular dichroism measurement revealed the groove binding of IPA to ctDNA and showed that the binding did not significantly change ctDNA confirmation. Furthermore, molecular docking found that IPA attached in the A-T rich minor groove region of the DNA. Molecular dynamics simulation showed that DNA and IPA formed a stable complex and IPA caused slight fluctuations for the residues at the binding site. Gel electrophoresis experiments showed that IPA did not significantly disrupt the DNA structure. These findings may provide useful information on the potential toxicological effects and environmental risk assessments of IPA residue in food at the molecular level.

Multispectroscopic and computational techniques to study the interaction of anthraquinone appended sensor with calf thymus DNA

An anthraquinone based derivative (AQ) has been designed and synthesized to find its applications for the interactions with calf thymus DNA (ctDNA) involving various spectroscopic techniques, thermodynamic and computational approaches. The UV-vis studies pointed to interaction of AQ with ctDNA via groove binding mode, which has been further supported well by the ionic strength studies, viscosity measurement, circular dichroism and melting temperature (Tm) curves. These findings have been further validated by dye-displacement assay and molecular docking studies. The analysis of thermodynamic parameters supports that the AQ-ctDNA binding is entropy favoured and enthalpy disfavoured and main acting binding interaction is hydrophobic interaction. The outcomes of the molecular modelling suggested that AQ might have entered the A-T abundant area of the ctDNA.Communicated by Ramaswamy H. Sarma.

Intercalation of anticancer drug Palbociclib with calf-thymus DNA: new insights from molecular spectroscopic, molecular dynamic simulations and cleavage studies

The interaction between the anti-cancer drug Palbociclib (PAL) and calf-thymus DNA (CT-DNA) was investigated using various biophysical techniques in a physiological buffer (pH 7.4). It was found that PAL intercalated into the base pairs of CT-DNA as evidenced from the results of UV-Vis, fluorescence, circular dichroism (CD), competitive binding assay with ethidium bromide (EB) and Hoechst 33258, KI quenching study, the effect of denaturing agent and viscosity measurements. The magnitude of binding constants (106 M-1) at different temperatures suggested strong binding between PAL and CT-DNA during complexation. The observed ΔHo > 0 and ΔSo > 0 indicated that the binding process is primarily driven by hydrophobic interactions. Molecular docking studies indicated partial intercalation of pyridopyrimidine ring between the base pairs of DNA. Free energy surface (FES) analysis derived from metadynamics simulation studies revealed the PAL-induced cleavage of DNA, which was confirmed by gel electrophoresis experiments.Communicated by Ramaswamy H. Sarma.

Experimental and theoretical investigations of Erbium complex: DNA/BSA interaction, anticancer and antibacterial studies

To assess the biological potential of an Er complex that contains a 2,2'-bipyridine ligand, various techniques such as multispectral and molecular modeling procedures were utilized to examine its DNA-binding ability, BSA binding affinity, antimicrobial effects, and anticancer properties. By analyzing fluorescent information and employing the vant' Hoff equation, important parameters such as the innate docking coefficient (Kb), Stern-Volmer coefficient (KSV), and thermodynamic properties including modifications in liberated energy (ΔG°), enthalpy (∆H°), and entropy (∆S°) were determined. The trial findings suggest that the compound can bind to DNA, primarily through groove binding. Additionally, the engagement between the Er compound and the protein BSA was examined using emission spectroscopy technique, revealing a powerful binding affinity between the compound and BSA. The Er complex binds to BSA primarily via hydrogen links and van der Waals forces, as indicated by the adverse values of ΔH° and ∆S°. Through a static quenching process, the complex significantly reduces the intrinsic fluorescence of BSA. Molecular binding calculations and rivalrous binding trials confirm that this compound dock to hydrophobic remains found in site III of BSA. Additionally, the Er complex demonstrates promising results in terms of its anticancer and antimicrobial activities based on screening tests.

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.

Study of Interactions Between 3-benzoyl-4-hydroxy-2-methyl-2H-1, 2-benzothiazine and Human DNA by Theoretical, Spectroscopic and Viscometric measurements

From the last few years mode of interactions between drugs and DNA is an attractive research area as it bridges chemistry, molecular biology and medicinal science. Interactions between small heterocyclic molecules and human DNA is a noteworthy feature in pharmacology for investigation of drugs mechanism and designing of more effective and target specific drugs with fewer side effects. The present research work focuses on the theoretical investigations of 3-benzoyl-4-hydroxy-2-methyl-2H-1, 2-benzothiazine (SASA) by using Gaussian (16 W) software to predict optimized geometry, HOMO-LUMO gap, bond length, bond angle, dihedral angle, electronic and vibrational spectra. Possible reaction site observed in SASA was C_7, C₉ and C₁₈ as these atoms show maximum charge density. Later the interactions of SASA with human DNA was explored spectroscopic investigations and viscometric investigations at physiological buffers of pH of 4.7 (stomach pH) and 7.4 (blood pH) respectively. Maximum absorbance between SASA-DNA complex was observed in buffer solution of pH 3.4 at wavelength of 370 nm, whereas at 7.4 has maximim absorbance between. Spectroscopic results reflects the bathochromic and hyperchromic shift succeeding the addition of human DNA. During viscosity measurement, intercalation and electrostatic mode of interaction were detected at low and high concentration of drug in solution respectively. Increase in the value of rate constant was observed with the increase in concentration of drug. Larger values of rate constant were observed at pH 7.4 in comparison to pH 3.5. Rate constant, thermodynamic parameters and viscometric analysis prefers the intake of SASA via blood.

Synthesis, Conformational Analysis and ctDNA Binding Studies of Flavonoid Analogues Possessing the 3,5-di-tert-butyl-4-hydroxyphenyl Moiety

Flavanones and their biochemical precursors, chalcones, are naturally occurring compounds and consist of privileged scaffolds used in drug discovery due to their wide range of biological activities. In this work, two novel flavanones (3 and 4), the arylidene flavanone 5, and the chalcone 6, displaying structural analogies with butylated hydroxytoluene (BHT), were synthesized via an aldol reaction. According to the antioxidant activity studies of the synthesized flavanones, the arylidene flavanone 5 was the most potent antioxidant (70.8% interaction with DPPH radical and 77.4% inhibition of lipid peroxidation). In addition, the ability of the synthesized compounds to bind with ctDNA was measured via UV-spectroscopy, revealing that chalcone 6 has the strongest interaction with DNA (Kb = 5.0 × 10−3 M−1), while molecular docking was exploited to simulate the compound-DNA complexes. In an effort to explore the conformational features of the novel synthetic flavanones (3 and 4), arylidene flavanone 5, and chalcone 6, theoretical calculations were applied and the calculation of their physicochemical properties was also performed.

Understanding the binding behavior of Malathion with calf thymus DNA by spectroscopic, cell viability and molecular dynamics simulation techniques: binary and ternary systems comparison

The interaction between calf thymus DNA (ctDNA) and Malathion in the absence and presence of Histone 1 has been enquired by the means of spectroscopic, viscometry, molecular modeling, and cell viability assay techniques. Malathion is capable of quenching the fluorescence of ct DNA in the absence and presence of H1. The binding constants of Malathion-ctDNA complex in the absence of H1 have been calculated to be 6.62 × 10⁴, 4.31 × 10⁴ and 1.93 × 10⁴ M^-1 at 298, 303, and 308 K, respectively that revealed static quenching in complex formation. The observed negative values of enthalpy and entropy changes indicate that the main binding interaction forces were van der Waals force and hydrogen bonding. The binding constant between Malathion and single-stranded ctDNA (ss ctDNA) seemed to be much weaker than that of Malathion and double-stranded ctDNA (ds ctDNA). Furthermore, Malathion can induce detectable alterations in the CD spectrum of ctDNA, along with changes in its viscosity. In the presence of H1, fluorescence quenching of ctDNA-Malathion complex displays dynamic behavior and binding constants were perceived to be 1.66 × 10⁴, 2.93 × 10⁴ and 5.77 × 10⁴ M^-1 at 298, 303, and 308 K, respectively. The different of interaction behavior between ctDNA and Malathion in the absence and presence of H1 clearly revealed H1 role in the complex formation and forces change between ctDNA and Malathion. The positive values of enthalpy and entropy changes have suggested that binding process is primarily driven by hydrophobic interactions. The tendency to interact with ss ctDNA, reduced viscosity have designated that the Malathion bound to ctDNA in the presence of H1 is groove binding. The results of molecular docking and molecular dynamics simulation also confirmed potent interactions between Malathion and the macromolecules in the binary and ternary systems.Communicated by Ramaswamy H. Sarma.

Electrochemical Detection of Linagliptin and its Interaction with DNA

Objectives

Linagliptin (Lin) is a drug used in treatment of type 2 diabetes mellitus. In this study, the electrochemical detection of Lin and its interaction with DNA was analyzed for the first time using voltammetric methods by measuring the oxidation currents of the adenine bases of DNA before and after the interaction. In addition, the electrochemical properties of the Lin were studied.

Materials and Methods

The interaction between Lin and DNA was evaluated using differential pulse voltammetry. A three-electrode system comprising of a pencil graphite electrode as the working electrode, reference electrode (Ag/AgCl), and platinum wire as the auxiliary electrode was used in the electrochemical studies. Experimental conditions, such as the concentration, pH of the supporting electrolyte, and immobilization time were optimized to obtain maximum analytical signals.

Results

The adenine bases of DNA were evaluated as an analytical signal obtained at approximately +1.2 V vs. Ag/AgCl. After the Lin-DNA interaction, the oxidation currents of adenine decreased as proof of interaction. No reports have been published on Lin interacting with DNA. Based on our results, a diffusion-controlled irreversible redox process involving independent oxidation was revealed for Lin. Under optimum conditions, the detection limit was 6.7 µg/mL for DNA and 21.5 µg/mL for Lin. Based on the observations, Lin has a toxic effect on DNA.

Conclusion

We successfully demonstrated that Lin interacts with DNA, and its influence on DNA could play a vital role in the medical effect of the drug.

DNA-binding activities of compounds acting as enzyme inhibitors, ion channel blockers and receptor binders

The DNA-binding activities of compounds used as remedies can display DNA-protection, but also damaging effects in biological systems. The current review compiles literature data on DNA-binding activities of drugs widely used as remedies with different therapeutic indications. The compounds are classified according their mechanism of action: enzyme inhibitors, ion channel inhibitors, inhibitors of viral RNA replication and HIV protease and receptor agonists. DNA binding was reported for such widely used drugs as paracetamol, aspirin, metformin, statins and many others. The capability of the drug to bind DNA is sometimes coupled to genotoxic effects, but in some cases - to genome protection. Data on atoms and chemical groups involved in the drug-DNA interactions are also presented. In many cases the same atoms are involved in both interactions of the compounds with proteins and DNA.

Exploring the Potential Mechanism of Costunolide-Induced MCF-7 Cells Apoptosis by Multi-Spectroscopy, Molecular Docking and Cell Experiments

Breast cancer is one of the most common cancer with high morbidity and mortality in women. This study aimed to explore the potential mechanism of costunolide inducing MCF-7 cells apoptosis by multi-spectroscopy, molecular docking, and cell experiments. The results manifested that costunolide interacted with calf thymus DNA (ct-DNA) in a spontaneous manner, and the minor groove as the preferential binding mode. Furthermore, costunolide inhibited cell proliferation and colony formation. Hoechst 33258 staining showed that cell apoptosis induced by costunolide might be related to DNA damage. The apoptosis mechanism relied on regulating the protein expression of Bax, Bcl-2, p53, Caspase-3 and the activation of p38MAPK and nuclear factor κB (NF-κB) pathways. This study will provide some experimental basis and potential therapeutic strategy for breast cancer treatment.

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.

Spectroscopic, computational and molecular docking study of Cu(ii) complexes with flavonoids: from cupric ion binding to DNA intercalation

Copper(ii) complexes with flavonoids as perspective therapeutic agents with DNA as a target molecule.

Synthesis, characterization and in vitro cytotoxicity studies of novel Cu(II) complex containing zonisamide drug: DNA interaction by multi spectroscopic and molecular docking methods

In this study, the Cu(II) complex with Zonisamide (ZNS) and 1, 10-Phenanthroline (Phen) ligands as an anticancer metallodrug was synthesized and characterized successfully by FT-IR, mass spectrometry, TGA, XPS, AAS, CHNSO, magnetic susceptibility and electrical conductivity. The interaction of Cu(II) complex with DNA was explored through a multi-spectroscopic approach such as fluorescence, UV-vis spectrophotometry, CD spectroscopy, and viscosity measurements. Molecular docking simulation was carried out to gain a deeper insight into the target site of DNA which interacted with the mentioned complex. The competitive binding tests with Hoechst 33258 showed that [CuCl₂(ZNS)(Phen)EtOH].H₂O can bind to the groove site of DNA. The calculated thermodynamic parameters, ΔS° = +201.15 J mol^-1K^-1 and ΔH° = +41.32 kJ mol^-1 confirm that the hydrophobic forces and hydrogen bonding play an essential role in the binding process. The experimental and molecular modeling results demonstrate that the Cu(II) complex binds to DNA through major groove binding. Moreover, the in vitro cytotoxic effects of [CuCl₂(ZNS)(Phen)EtOH].H₂O against B92 cancer cell lines showed better activity in Cu(II) complex in comparison to free ZNS. Therefore, [CuCl₂(ZNS)(Phen)EtOH].H₂O can open a new horizon in the treatment of glioma cancer by ZNS metallodrugs.Communicated by Ramaswamy H. Sarma.

Probing the Strength and Mechanism of Binding Between Amifampridine and Calf Thymus DNA

In this work, we have investigated the strength and mechanism of amifampridine (3,4-Diaminopyridine/3,4-DAP) interaction with calf thymus DNA (ct-DNA). The existence and the strength of interaction are evaluated using circular dichroism (CD), UV-vis absorption, and differential pulse voltammogram studies. Results from UV-vis absorption technique indicate that amifampridine can significantly interact with DNA through a binding constant of Kb = 1.66 × 105 M-1 at 298 K. The mechanism of the interaction between amifampridine and DNA is also studied using ionic effect investigations, competitive fluorescence experiments, viscosity measurements, and molecular docking studies. The viscosity results indicate that amifampridine can bind to DNA via intercalation binding mode. Competitive fluorescence experiments using Acridine Orange (AO) and Hoechst 33258 (HO) probes also reveal that amifampridine binds to DNA via an intercalation mode of binding. Finally, the molecular docking studies also suggest that amifampridine tends to bind with the G-C rich region of DNA.

Hydrothermal synthesis and characterization of magnetic Fe3O4 and APTS coated Fe3O4 nanoparticles: physicochemical investigations of interaction with DNA

Magnetic nanoparticles (MNPs) especially iron oxide (Fe₃O₄) NPs have quite extensively been used for in vivo delivery of biomolecules and drugs because of their high bioconjugation efficiency. In this study, Fe₃O₄ NPs and (3-Aminopropyl) triethoxysilane (APTS) coated Fe₃O₄ NPs were synthesized and their interaction with Calf thymus (Ct) DNA has been studied in order to understand their usage in biomedical applications. Hydrothermal method was used for the NPs synthesis. Characterization of NPs was done using techniques like UV-Visible spectroscopy, FTIR spectroscopy, FE-SEM, EDAX, Zeta Sizer and powder XRD. Further, interaction studies of NPs with Ct-DNA were investigated using various physicochemical techniques. In UV-Visible studies, hypochromicity with binding constant 3.2 × 10⁵ M^-1 was observed. Binding constants calculated using fluorescence studies were found to be k = 3.2 × 10⁴ M^-1, 2.9 × 10⁴ M^-1 at 293 and 323 K respectively. Results of UV-Visible and fluorescence studies were in correlation with other techniques like UV-T_M and CD. All studies suggested alteration in DNA conformation on interaction with surface engineered Fe₃O₄ NPs, stabilizing DNA-NPs conjugate via partial intercalation and electrostatic interactions. This study may facilitate our understanding regarding the physicochemical properties and DNA-binding ability of APTS-Fe₃O₄ NPs for their further application in magnetosensitive biosensing and drug delivery. Iron oxide based magnetic nanoparticles are well known for their excellent bio-conjugation efficiency and therefore APTS-Fe₃O₄ NPs were synthesized via very simple and benign hydrothermal method. Further, the interaction of APTS-Fe₃O₄ NPs with calf thymus DNA was studied using various physicochemical techniques to explore their potential in biomedical applications.

Flow microdialysis sampling-chemiluminescent detection coupled with molecular docking for the investigation of binding behavior between salbutamol and DNA

The investigation of the binding behavior between drug and DNA provides basic information for understanding pharmacological and toxicologic mechanisms of many drugs. Herein, a facile chemiluminescent (CL) method for investigating the binding behavior between salbutamol and calf thymus DNA (ct-DNA) was established by utilizing flow microdialysis sampling technique. In a reaction equilibrium solution of salbutamol and ct-DNA, free salbutamol was extracted by a microdialysis probe, and then injected into a flow-injection CL detection system to quantitate its concentration. The binding constants of salbutamol acquired by Klotz analysis and Scatchard analysis were 2.97 × 10⁴ M^-1and 2.99 × 10⁴ M^-1, respectively. Salbutamol showed one sort of binding site on ct-DNA. Meanwhile, the three-dimensional spatial structure of the binding mode was investigated by molecular docking. The results indicate that the binding mode of salbutamol to ct-DNA was groove binding. The hydrogen bonds were primary driving force for the direct recognition of salbutamol by ct-DNA. This proof-of-principle method paves a pathway to investigate the binding behavior between small-molecular drug and DNA, and provides a theoretical guidance for designing DNA-targeting drugs.

Experimental and theoretical investigations of Dy(III) complex with 2,2'-bipyridine ligand: DNA and BSA interactions and antimicrobial activity study

In this study, the interactions of a novel metal complex [Dy(bpy)₂Cl₃.OH₂] (bpy is 2,2'-bipyridine) with fish salmon DNA (FS-DNA) and bovine serum albumin (BSA) were investigated by experimental and theoretical methods. All results suggested significant binding between the Dy(III) complex with FS-DNA and BSA. The binding constants (K_b), Stern-Volmer quenching constants (K_SV) of Dy(III)-complex with FS-DNA and BSA at various temperatures as well as thermodynamic parameters using Van't Hoff equation were obtained. The experimental results from absorption, ionic strength, iodide ion quenching, ethidium bromide (EtBr) quenching studies and positive ΔH˚ and ΔS˚ suggested that hydrophobic groove-binding mode played a predominant role in the binding of Dy(III)-complex with FS-DNA. Indeed, the molecular docking results for DNA-binding were in agreement with experimental data. Besides, the results found from experimental and molecular modeling indicated that the Dy(III)-complex bound to BSA via Van der Waals interactions. Moreover, the results of competitive tests by phenylbutazone, ibuprofen, and hemin (as a site-I, site-II and site-III markers, respectively) considered that the site-III of BSA is the most possible binding site for Dy(III)-complex. In addition, Dy(III) complex was concurrently screened for its antimicrobial activities. The presented data provide a promising platform for the development of novel metal complexes that target nucleic acids and proteins with antimicrobial activity.Communicated by Ramaswamy H. Sarma.

Molecular docking and spectroscopic studies on the interaction of new fifth-generation antibacterial drug ceftobiprole with calf thymus DNA

The interaction of the cefobiprole drug with calf thymus DNA (ct-DNA) at physiological pH was investigated by UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, circular dichroism spectroscopy and molecular modeling. The binding constant obtained of UV-visible was 4 × 10⁴ L mol^-1. Moreover, the results of circular dichroism (CD) and viscosity measurements displayed that the binding of the cefobiprole to ct-DNA can change the conformation of ct-DNA. Furthermore, thermodynamic parameters indicated that hydrogen bond and van der waals play main roles in the binding of cefobiprole to ct-DNA. Optimal results of docking, it can be concluded that ceftobiprole-DNA docked model is in approximate correlation with our experimental results.

In vitro investigating of anticancer activity of new 7-MEOTA-tacrine heterodimers

A combination of biochemical, biophysical and biological techniques was used to study calf thymus DNA interaction with newly synthesized 7-MEOTA-tacrine thiourea 12-17 and urea heterodimers 18-22, and to measure interference with type I and II topoisomerases. Their biological profile was also inspected in vitro on the HL-60 cell line using different flow cytometric techniques (cell cycle distribution, detection of mitochondrial membrane potential dissipation, and analysis of metabolic activity/viability). The compounds exhibited a profound inhibitory effect on topoisomerase activity (e.g. compound 22 inhibited type I topoisomerase at 1 µM concentration). The treatment of HL-60 cells with the studied compounds showed inhibition of cell growth especially with hybrids containing thiourea (14-17) and urea moieties (21 and 22). Moreover, treatment of human dermal fibroblasts with the studied compounds did not indicate significant cytotoxicity. The observed results suggest beneficial selectivity of the heterodimers as potential drugs to target cancer cells.

Exploring the binding interaction of Maillard reaction by-product 5-hydroxymethyl-2-furaldehyde with calf thymus DNA

BACKGROUND

5-Hydroxymethyl-2-furaldehyde (5-HMF), a by-product of the Maillard reaction, usually present in fried and baked food, may cause potential harm to the human body. Here, the interaction between 5-HMF and calf thymus DNA (ctDNA) under physiological buffer (pH 7.4) was studied using multi-spectroscopic methods combined with multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics and molecular simulation techniques.

RESULTS

The concentration profiles and pure spectra of the three components (5-HMF, ctDNA and 5-HMF-ctDNA complex) were extracted from highly overlapping spectra using MCR-ALS analysis, which verified the formation of 5-HMF-ctDNA complex. The binding constant being of the order of 10³  L mol^-1 at four temperatures (292, 298, 304 and 310 K) indicated a weak affinity in the binding of 5-HMF to ctDNA. The binding interaction was mainly driven by hydrogen bonds and van der Waals forces. Viscosity analysis, melting assay, ionic strength effect and competitive fluorescence studies ascertained that 5-HMF bound to ctDNA through groove binding, and it tended to bind to guanine-cytosine rich region of ctDNA which was characterized using Fourier transform infrared spectra and molecular docking. Circular dichroism spectral analysis and DNA cleavage assays indicated that the ctDNA conformation was altered from B to A form and 5-HMF caused DNA damage at higher concentration.

CONCLUSIONS

The results suggested that 5-HMF bound to ctDNA through groove binding and caused DNA damage. This research may contribute to understand the binding mechanism of 5-HMF to ctDNA and to the assessment of the toxicological effect of 5-HMF in biological processes. © 2018 Society of Chemical Industry.

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.

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.

Binding studies of guggulsterone-E to calf thymus DNA by multi-spectroscopic, calorimetric and molecular docking studies

Guggulsterone, a sterol found in plants is used as an ayurvedic medicine for many diseases such as obesity, internal tumors, ulcers etc. E and Z are two isoforms of guggulsterone, wherein guggulsterone-E (GUGE) has also been shown to have anticancer potential. Most of the anticancer drugs target nucleic acids. Therefore, we studied the mode of interaction between ctDNA and GUGE using UV-Vis, fluorescence and CD spectroscopy, isothermal calorimetry along with molecular docking studies. Hoechst 3325, ethidium bromide and rhodamine-B displacement experiments confirms that GUGE binds in the minor groove of DNA. ITC results further suggest these interactions to be feasible and spontaneous with hydrogen bond formation and van der waals interactions. Lastly, molecular docking also suggests GUGE to be a minor groove binder interacting through a single hydrogen bond formation between OH group of GUGE and nitrogen (N3) of adenosine (A6).

Peptide-Based Polymer-Polyoxometalate Supramolecular Structure with a Differed Antimicrobial Mechanism

Because of the increasing prevalence of multidrug resistance feature, several investigations have been so far reported regarding the antibiotic alternative supramolecular bioactive agents made of hybrid assemblies. In this regard, it is well-established that combinational therapy inherited by assembled supramolecular structures can improve the bioactivity to some extent, but their mode of action has not been studied in detail. We provide first direct evidence that the improved mechanism of action of antimicrobial supra-amphiphilic nanocomposites differs largely from their parent antimicrobial peptide-based polymers. For the construction of a hybrid combinational system, we have synthesized side-chain peptide-based antimicrobial polymers via RAFT polymerization and exploited their cationic nature to decorate supra-amphiphilic nanocomposites via interaction with anionic polyoxometalates. Because of cooperative antimicrobial properties of both the polymer and polyoxometalate, the nanocomposites show an enhanced antimicrobial activity with a different antimicrobial mechanism. The cationic stimuli-responsive peptide-based polymers attack bacteria via membrane disruption mechanism, whereas free radical-mediated cell damage is the likely mechanism of polymer-polyoxometalate-based supra-amphiphilic nanocomposites. Thus, our study highlights the different antimicrobial mechanism of combinational systems in detail, which improves our understanding of enhanced antimicrobial efficacy.

Binding affinity of pyrano[3, 2-f]quinoline and DNA: spectroscopic and docking approach

The interaction between pyrano[3, 2-f]quinoline (PQ) and calf thymus DNA (CTDNA) using spectroscopic and molecular modeling approach has been presented here. Apparent association constant (1.05×10⁵ L/mol) calculated from UV-vis specta, indicates a moderate complex formation between CTDNA and PQ. The quenching phenomena as obtained from emission spectra of ethidium bromide (EB)-CTDNA by PQ was found to be a dynamic one and the binding constants found to be 8.64, 9.25, 11.17, 12.03 × 10⁴ L/mol at 293, 300, 308, and 315 K. Thermodynamic parameter enthalpy change (ΔH) and entropy change (ΔS), indicates weak force like van der Walls force and hydrogen bonds having the key role in this binding process. The results of circular dichroism (CD) demonstrate that PQ has not induced characteristic changed in CTDNA. Results achieved from UV absorption and fluorescence spectroscopy indicating the binding mode of PQ with DNA seems to be a nonintercalative binding. The theoretical results as originating from molecular modeling showed that PQ possibly will bind into the hydrophobic region of DNA having docking binding energy = -10.03 kcal/mol and the obtained results are in consonance with the inferences obtained from experimental data. This result is important for the better understanding of pharmaceutical aspects of binding affinity of PQ and CTDNA.