Antimicrobial, cytotoxicity, molecular modeling and DNA cleavage/binding studies of zinc-naproxen complex: switching DNA binding mode of naproxen by coordination to zinc ion

The intercalation DNA binding mode of the naproxen, a non-steroidal anti-inflammatory drug, has been reported previously. In this study, calf thymus deoxyribonucleic acid (CT-DNA) binding of zinc-naproxen complex, [Zn(naproxen)₂(MeOH)₂], at physiological pH has been investigated by multi-spectroscopic techniques and molecular docking. Zinc-naproxen complex displays significant binding property to the CT-DNA (K_b = 0.2 × 10⁵ L.mol^-1). All of the experimental results; relative increasing in viscosity of CT-DNA and fluorimetric studies using ethidium bromide (EB) and Hoechst 33258 probes, are indicative of groove binding mode of zinc-naproxen complex to CT-DNA. These results show that the coordination of naproxen to zinc metal switches the mode of binding from intercalation to groove. The molecular modeling also shows that the complex binds to the AT-rich region of minor groove of DNA. Structural and topography changes of DNA in interaction with the complex by atomic force microscopy (AFM) indicated that CT-DNA becomes swollen after interaction. The pUC18 plasmid DNA cleavage ability of zinc-naproxen complex by gel electrophoresis experiments revealed that zinc-naproxen complex cleaved supercoiled pUC18 plasmid DNA to nicked DNA. The cytotoxicity of the zinc complex performed by MTT method on HT29 and MCF7 cancer cell lines and on HEK 293 normal cell lines indicates that zinc complex has no cytotoxic effect on both HT29 and MCF7 cell lines but has better cytotoxicity effect on HEK 293 cell lines compared to cisplatin standard drug. The antimicrobial activity of the complex against Staphylococcus aureus and Escherichia coli bacteria revealed the high antimicrobial activity of the complex.Communicated by Ramaswamy H. Sarma.

In vitro cytotoxicity studies of smart pH-sensitive lamivudine-loaded CaAl-LDH magnetic nanoparticles against Mel-Rm and A-549 cancer cells

In this study, an effective nano-drug delivery system was prepared by the co-precipitation method via two steps; the preparation of Fe₃O₄ magnetic nanoparticles and its surface modification with layered double hydroxide (LDH) and loading lamivudine on this nanocarrier (Fe₃O₄@CaAl-LDH@Lamivudine). The developed nanoparticles (NPs) were characterized by X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy, energy dispersive X-ray analysis, Fourier-transformed infrared spectroscopy, vibrating-sample magnetometry, thermogravimetric analysis, X-ray photoelectron spectroscopy and Brunauer-Emmett-Teller. The prepared system demonstrated an average size of 130 nm. Also, the drug entrapment efficiency was estimated at ∼70%. In vitro, drug release investigations showed a controlled and pH-dependent lamivudine release over 300 min. The in vitro cytotoxic activity of Fe₃O₄@CaAl-LDH@Lamivudine NPs was explored against Mel-Rm and A-549 cancer cell lines in comparison with lamivudine and nanocarrier using lactate dehydrogenase colorimetric and MTT assay. The results of the MTT assay revealed that the Fe₃O₄@CaAl-LDH@Lamivudine NPs significantly inhibited the proliferation of Mel-Rm and A-549 cells in a dose-dependent manner. The influences of Fe₃O₄@CaAl-LDH@Lamivudine on the cancer cell lines by different therapeutic investigation illustrated the remarkable effect in comparison with free drug. Finally, the achieved consequences confirm the anticancer properties of Fe₃O₄@CaAl-LDH@Lamivudine and indicate that they may be a cost-effective substitute in the treatment of lung and skin cancer.Communicated by Ramaswamy H. Sarma.

Exploring the binding mechanisms of inorganic magnetic nanocarrier containing L-Dopa with HSA protein utilizing multi spectroscopic techniques

In this study, the interaction of Fe₃O₄@CaAl-LDH@L-Dopa nanoparticles (NPs) with human serum albumin (HSA) was investigated in simulated physiological conditions applying UV-visible, fluorescence, and circular dichroism (CD) spectroscopic techniques. The consequences of UV-vis and CD spectroscopy demonstrated that the interaction of HSA to Fe₃O₄@CaAl-LDH@L-Dopa NPs enforced some conformational alterations within HSA. The fluorescence spectroscopy analysis indicated that by enhancing temperature, the Stern-Volmer quenching constant (K_sv) was decreased, which is relevant to a static quenching mechanism. The binding constant (K_b) was 7.07 × 10⁴ M^-1 while the number of the binding site (n) was 0.94 which is in compromise with its binding constant. Also, thermodynamic parameters (ΔH° > 0, ΔG° < 0, and ΔS° > 0) have suggested that hydrophobic forces perform a key role in the interaction of HSA with Fe₃O₄@CaAl-LDH@L-Dopa NPs. Displacement studies successfully carried out using the Warfarin and Ibuprofen have predicted that the binding of Fe₃O₄@CaAl-LDH@L-Dopa NPs to HSA is situated at site II (subdomain IIIA).Communicated by Ramaswamy H. Sarma.

In vitro interaction of nucleoside reverse transcriptase inhibitor, didanosine with calf-thymus DNA: Insights from spectroscopic studies

Many antivirals interact with DNA and alter their expression profile. Thus, it is necessary to understand the binding mode. Didanosine, a nucleoside reverse transcriptase inhibitor, is used to treat HIV infection in patients with or without acquired immunodeficiency syndrome. Understanding the mechanism of interaction of this nucleoside reverse transcriptase inhibitor with DNA can prove useful in the development of a rational drug designing system. In vitro studies (UV-vis, fluorescence, and viscometry techniques) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) show that didanosine drug interacts with calf-thymus DNA (ct-DNA) via partial intercalative binding mode. UV-visible spectroscopy confirmed the formation didanosine-DNA complex with a binding strength of about 1.5 × 10⁵ M^-1 thus indicating their biological worth. Dye displace experiments and viscometry confirmed that didanosine partially intercalates toward DNA molecules. Negative value of Gibb's-free energy change revealed that the process is spontaneous. The thermodynamic parameters such as enthalpy change (ΔH) and entropy change (ΔS) showed that the acting forces between didanosine and ct-DNA mainly included hydrophobic interactions.

Equilibrium and site selective analysis for DNA threading intercalation of a new phosphine copper(I) complex: Insights from X-ray analysis, spectroscopic and molecular modeling studies

To clarify the interaction of phosphine copper(I) complex with DNA, our study reports the synthesis of a new phosphine copper(I) complex, along with a detailed analysis of the geometry characterization and its interaction with double-stranded DNA. The triclinic phase Cu(PPh₃)₂(L)(I) with a tetrahedral geometry was identified as the product of the reaction of copper(I) iodide with (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] ligand and triphenylphosphine by single-crystal X-ray analysis. Molecular interaction of the synthesized complex with the calf thymus deoxyribonucleic acid (ct-DNA) was investigated in the physiological buffer (pH 7.4) by multi-spectroscopic approaches associated with a competitive displacement towards Hoechst 33258 and methylene blue (MB) as groove and intercalator probes. The fluorescence and UV/Vis results detected the formation of a complex-DNA adduct in the ground-state with a binding affinity in order of 10⁴ M^-1, which is in keeping with both groove binders and intercalators. The thermodynamic parameters, ΔS⁰ = -200.31 ± 0.08 cal/mol·K and ΔH⁰ = -63.11 ± 0.24 kcal/mol, confirmed that the van der Waals interaction is the main driving force for the binding process. Moreover, the ionic strength and pH effect experiments demonstrated the electrostatic interactions between the complex and DNA is negligible. Analysis of the molecular docking simulation declared the flat (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] part of the complex was inserted between the sequential A…T/A…T base pairs, while the phosphine substituents were located in the groove, i.e. threading intercalation. Besides, the cytotoxicity of the complex against the MCF-7 human breast cancer cells was detected at IC50 = 10 μg/mL.

Multispectroscopic analysis, atomic force microscopy, molecular docking and molecular dynamic simulation studies of the interaction between [SnMe2Cl2(Me2phen)] complex and ct-DNA in the presence of glucose

In this study, the spectroscopic methods (UV-vis, fluorimetric), Atomic force microscopy, and computational studies (molecular docking and molecular dynamic simulation) were used to investigate the interaction of [SnMe₂Cl₂(Me₂phen)] complex with CT-DNA in the presence of glucose. The results showed the complex in the medium containing glucose has less effect on calf thymus DNA (ct-DNA) than the medium without glucose. Cytotoxicity of [SnMe₂Cl₂(Me₂phen)] complex on MCF-7 cells was examined and showed Sn(IV) complex possesses potential cytotoxicity against this cell line. Molecular docking study showed that Sn(IV) complex interacts with DNA by groove binding mode. Radius of gyration (Rg) was smaller upon binding of the Sn(IV) complex suggesting a more compact structure of DNA in the presence of Sn(IV) complex.Communicated by Ramaswamy H. Sarma.

In vitro spectroscopic investigation of groove binding interaction of Fe3O4@CaAl-LDH@L-Dopa with calf thymus DNA

The principal goal of this study is to evaluate the interaction of Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles with calf thymus DNA. The magnetic nanoparticles were previously prepared by a chemical co-precipitation method, and the surface of the Fe₃O₄ nanoparticles was coated with CaAl layered double hydroxides. The antiparkinsonian drug "L-Dopa" was carried by this core-shell nanostructure to achieve the drug delivery system with suitable properties for biological applications. Also, the interaction of Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles with CT-DNA was studied using, UV-Visible spectroscopy, viscosity, circular dichroism (CD), and fluorescence spectroscopy techniques. The results of investigations demonstrated that Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles have interacted via minor groove binding and intercalated to CT-DNA, respectively.

Evaluation of ct-DNA and HSA binding propensity of antibacterial drug chloroxine: Multi-spectroscopic analysis, atomic force microscopy and docking simulation

In the present study, the binding interactions of chloroxine, an antibacterial drug and antibiotic agent with calf thymus-deoxyribonucleic acid (ct-DNA) and human serum albumin (HSA) have been deliberated under simulative physiological conditions (pH = 7.40) employing multiple biophysical, atomic force microscopy and molecular modeling approaches. The ct-DNA binding properties of chloroxine exhibit that it binds to ct-DNA through a groove binding mode, and the binding constant values were computed employing the absorption and emission spectral data. The fluorescence study shows the presence of the static quenching mechanism in the ct-DNA- chloroxine interaction. These results are further supported by UV-vis spectra. Large complexes contain the ct-DNA chains with an average size of 225.45 nm were observed by employing AFM for chloroxine -ct-DNA. The results revealed that the fluorescence quenching of albumin by chloroxine was a static quenching process as a result of albumin-chloroxine (1:1) complex. The distance between chloroxine and albumin was obtained based on the Förster's theory of non-radiative energy transfer. The results of AFM, synchronous and three-dimensional fluorescence spectra all revealed that chloroxine induced the conformational changes of albumin. Molecular docking technology represents the binding of chloroxine to the major groove of ct-DNA and site I (subdomain II A) of albumin.

Direct effects of low-energy electrons on including sulfur bonds in proteins: a second-order Møller-Plesset perturbation (MP2) theory approach

In an attempt to describe how low-energy electrons (LEEs) damage the polypeptide chain at disulfide bridges, ab initio electronic structure estimates on LEE interactions with cysteine-cysteine (Cys-Cys) disulfide bond model have been performed. Here, the fundamental mechanisms in LEE impression on S-S and C-S bond ruptures in the Cys-Cys model have been discussed. The electronic energy was calculated using the MP2 method with a Hartree-Fock exchange during the SCF and the Møller-Plesset correlation energy correction on the converged HF orbitals with 6-311++G(d,p) atomic orbital basis set. Further, six more sets of diffuse s and p functions with extra basis on the sulfur and relevant carbon atoms were used to describe the added electron to located away as much as possible from the nuclei in anions. The bonds rupture mechanisms involve the primary placement of LEEs to the π* orbital of the model to construct the shape-resonance state following by an adiabatic or nonadiabatic electron migration to either S-S or C-S bond σ* orbital. The formed radical anion undergoes S-S or C-S bonds cleavage by energy barriers of ca. 5.68 and 9.19 kcal/mol, respectively, to produce either (2-amino-2-carboxyethyl) sulfanyl (cysteine radical), aziridine-2-carboxylic acid or mercapto-L-cysteine lesions. In SMD solvent, calculations suggest electronically stable of the formed π* and σ* states by solvation, something that induces either S-S or C-S bond break even when the electron energy is near zero. The required barrier energy of only 0 to < 0.4 eV indicates a high kinetic favorable fragmentation for involved sulfur polypeptides with LEEs.Communicated by Ramaswamy H. Sarma.

Synthesis of nano zinc-based metal-organic frameworks under ultrasound irradiation in comparison with solvent-assisted linker exchange: Increased storage of N2 and CO2

Isostructural nano Zn(II)-based metal-organic frameworks (MOFs), Zn-TMU, has been synthesized by ultrasound process and solvent-assisted linker exchange (SALE). Zn(II)-MOFs were investigated as CO₂ capture compounds. Compared with ultrasound process, the as-prepared daughter frameworks showed enhanced CO₂ sorption capacity, ascribed to the existence of structural defects during the SALE method. This study demonstrated that the gas storage depends mainly on the quality and defects in the structure, which depends on the synthetic conditions. This study is a new report of increasing CO₂ sorption in Zn-TMU by a SALE method.

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).

Intercalation of manganese-mefenamic acid complex into double stranded of calf thymus DNA

The interaction of the [Mn(mef)₂(phen)H₂O] complex in which mef is mefenamic acid drug and phen is 1,10 phenanthrolin ligand with calf thymus DNA (ct-DNA) was studied by using different spectroscopic methods, molecular docking and viscometery. The competitive fluorescence and UV-Vis absorption spectroscopy indicated that the complex interacted with ctDNA via intercalating binding mode with the binding constant of 1.16 × 10⁴ Lmol^-1. The thermodynamic studies showed that the reaction between the complex and ctDNA is exothermic. Furthermore, the complex induced changes in DNA viscosity. Circular dichroism spectroscopy (CD) was employed to measure the conformational changes of ctDNA in the presence of the complex and verified intercalation binding mode. The molecular modeling results illustrated that the complex interacted via intercalation by relative binding energy of -28.45 kJ mol^-1.

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.

Antiproliferative effects of new magnetic pH-responsive drug delivery system composed of Fe3O4, CaAl layered double hydroxide and levodopa on melanoma cancer cells

In this study, an efficient drug delivery system composed of Fe₃O₄, CaAl layered double hydroxide (LDH) and l-Dopa has been synthesized through hydrogen bonds between l-Dopa and CaAl-LDH encapsulated Fe₃O₄ nanoparticles (Fe₃O₄@CaAl-LDH@l-Dopa). The structural features of Fe₃O₄@CaAl-LDH@l-Dopa were characterized using XRD, SEM, TEM, EDX, FT-IR, VSM, TGA, XPS, zeta potential analysis and BET. All of the characterization techniques show the uniform high surface area core-shell structure with about 120 nm in average size. Also, the obtained results clearly indicate that this drug delivery system possess high potent for adsorption of l-Dopa (52 wt%) and high drug encapsulation efficiency (71%). The amount of l-Dopa release in low pHs (53.8%) which simulates the environment of cancer cells is greater than higher pHs. The in vitro cytotoxic and anticancer activities of Fe₃O₄@CaAl-LDH@l-Dopa were investigated against Mel-Rm Cells Melanoma (NCIt: C3224) using LDH colorimetric assay and differential staining cell death assay. The results showed Fe₃O₄@CaAl-LDH@l-Dopa with a lower concentration of l-Dopa, illustrate a higher cytotoxicity and anticancer activity.

Synthesis, characterization and DNA interaction studies of new copper complex containing pseudoephedrine hydrochloride drug

A new copper(II) complex, [Cu(pse)(phen)Cl₂]; in which phen = 1,10-phenanthroline and pse = pseudoephedrine hydrochloride drug; was synthesized and characterized by FT-IR, Mass and UV-Vis spectroscopy in combination with computational methods. Binding interaction of this complex with calf thymus DNA (ct-DNA) has been investigated by absorption, emission, circular dichroism, molecular docking and viscosity measurements. The complex displays significant binding properties of ct-DNA. The results of fluorescence and UV-Vis absorption spectroscopy indicated that, this complex interacted with ct-DNA in a groove-binding mode, and the binding constant was 8 × 10⁴ L mol^-1. Competitive fluorimetric studies with Hoechst 33258 have shown that Cu(II) complex exhibit the ability to displace the DNA-bound Hoechst 33258 indicating that it binds to DNA in strong competition with Hoechst 33258 for the groove binding. Furthermore, the complex induces detectable changes in the CD spectrum of ct-DNA and does not induce any changes in DNA viscosity which verified the groove-binding mode. The molecular modeling results illustrated that the complex strongly binds to groove of DNA by relative binding energy of docked structure (-27.61 kJ mol^-1).

DNA binding studies of antibiotic drug cephalexin using spectroscopic and molecular docking techniques

The purpose of this study was to explore an accurate characterization of the binding interaction of antibiotic drug cephalexin with calf thymus DNA (CT-DNA) as a relevant biological target by using UV absorption, fluorescence spectroscopy and circular dichroism (CD) in vitro under simulated physiological conditions (pH = 7.4) and also through a molecular modeling study. The results showed that the drug interacts with the DNA helix via a minor groove binding mode. The thermodynamic parameters were calculated and showed that the reaction between the drug and CT-DNA was exothermic. In addition, the drug enforced traceable changes in the viscosity of DNA. The molecular modeling results indicated that cephalexin forcefully binds to the minor groove of DNA with a relative binding energy of -21.02 kJ mol^-1. The obtained theoretical results were in good agreement with those obtained from experimental studies.

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

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