Experimental and molecular modeling studies on the DNA-binding of diazacyclam-based acrocyclic copper complex

Comparative Linkage of Novel Anti-Tumor Pd(II) Complex with Bio-Macromulecules: Fluorescence, UV-Vis, DFT, Molecular Docking and Molecular Dynamics Simulation Studies

A novel mononuclear palladium complex, [Pd(dach)(SSA)], where dach and SSA are diaminocyclohexane and sulfosalicylic acid ligands, respectively, has been synthesized and identified utilizing analytical and spectral methods. DFT calculations, namely geometry optimization, MEP, HOMO-LUMO and NBO analysis, have been conducted at B3LYP level by aug-ccpVTZ-PP and 6-311G(d, p) basis sets. NBO and HOMO-LUMO analysis exhibited that the palladium compound is stable. MEP showed the potential sites of molecule for the interaction. By employing MTT assay, the cytotoxicity activity of the aforesaid compound was examined on K562 cell line, which revealed a proper activity compared to cisplatin. To ascertain the lipophilicity of the newly made compound, the partition coefficient measurement was accomplished, which follows the order of cisplatin < Pd(II) complex. Next, investigation of binding properties of the studied compound with DNA of calf thymus and BSA were done by spectroscopic (CD, fluorescence emission and electronic adsorption) and non-spectroscopic (viscosity measurements, DNA gel electrophoresis, molecular docking and molecular dynamics simulation) methods. The outcomes of CD and UV-Vis spectroscopy demonstrated that the title compound refolded the protein via increasing the alpha helix percentage. The data obtained from UV-Vis studies indicated the non-intercalative mutual action between Pd(II) complex with DNA. It also revealed that the Kapp magnitude of CT-DNA (7.43 × 104 M- 1) is higher than the BSA (5.17 × 103 M- 1), and L1/2 (midpoint of transition) of CT-DNA (5 µM) is lower than the BSA (5.7 µM), indicating that the complex has a greater binding affinity to CT-DNA than BSA. Fluorescence quenching mechanism of the two biomolecules by the metal complex is static and the calculated thermodynamic parameters (ΔS° < 0 and ΔH° < 0) suggested the hydrogen bonding and/ or van der Waals forces with DNA and BSA. Further, molecular docking indicated that the studied compound fits into the groove of DNA and the site I of BSA. The stability of metal compound-DNA/-BSA in the presence of H2O solvent and over the time were validated via molecular dynamics simulation.

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.

Studying the interaction between the new neodymium (Nd) complex with the ligand of 1,10-phenanthroline with FS-DNA and BSA

To learn more about the chemotherapeutic and pharmacokinetic properties of a neodymium complex containing 1,10-phenanthroline (dafone), In vitro binding was investigated with bovine serum albumin and fish-salmon DNA, using a variety of molecular modeling research and biophysical approaches. A variety of spectroscopic techniques including fluorescence and absorption were used to investigate the interplay between DNA/BSA and the neodymium complex. The findings revealed that the Nd complex had a high affinity for BSA and DNA interplays through van der Waals powers. In addition, the binding of the Nd complex to FS-DNA mainly in the groove binding mode clearly reflects with iodide quenching studies, ethidium bromide (EtBr) exclusion assay, ionic strength effect, and viscosity studies. It was observed that the Nd complex binds to FS-DNA through a minor groove with 3.81 × 105 (M-1). Also, Kb for BSA at 298 K was 5.19×105 (M-1), indicating a relatively high affinity of the Nd complex for DNA and BSA. In addition, a competitive study of a docking investigation revealed that the neodymium complex interacts at BSA site III. The results obtained from the binding calculations are well consistent with the experimental findings. Also, cytotoxicity studies of Nd complex were performed in MCF-7 and A-549 cell lines and the results show that this new complex has a selective inhibitory effect on the growth of various cancer cells.

The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study

In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.

Interactional, Functional and Biological Properties of Lactone Sophorolipid (LSL) and Collagen Oligopeptides (COP) in Aqueous Solution

For the mixed aqueous solution of LSL and COP, the interaction mode and mechanism have been comprehensively studied using multispectral methods including fluorescence spectrum, ultraviolet-visible adsorption spectrum (UV-Vis), and circular dichroism spectrum (CD). Then its surface activity, particle size, foaming, emulsifying, viscosity, and antibacterial properties are evaluated in detail by surface tension measurement (ST), dynamic light scattering (DLS), oscillametric method, spectrophotometer, ubbelohde viscometer and zone of inhibition separately. Compared with the single LSL or COP aqueous solution, the mixed system shows different performance optimizations in different aspects. The surface activity and foaming properties are mainly attributed to LSL, and the viscosity is attributed to COP. Fluorescence spectroscopy results show that the fluorescence distribution of COP has significant changes by the LSL addition and a static quenching mechanism is proved. The results of UV-Vis and CD spectra also show the changing conformation of COP by the LSL addition. The data of thermodynamic parameters prove that the combination of LSL and COP is a spontaneous exothermic process and is an enthalpy-driven process. The interaction mechanism between LSL and COP is very helpful for the application and development of the mixed mild biosurfactant-protein system used in the cosmetic and food industries.

Mechanism of interactions between soyasaponins and soybean 7S/11S proteins

In this study, the proteins glycinin (11S) and β-conglycinin (7S) were mixed with soyasaponin (Ssa) Ab/Bb to form a composite system. We used fluorescence and synchronous fluorescence spectra to demonstrate the changes in the surrounding environment and the structure of the proteins. Dynamic interface behavior analysis showed the possible interface behavior induced by the composite system. The interactions between Ssa and the proteins, along with the mode of action, were analyzed by molecular docking. The interactions between Ssa and soy protein increased with the change in concentration. The interactions between the two proteins were mediated by tryptophan (Trp) and primarily involved hydrogen bonds, which changed the microenvironment and loosened the protein structure. These results helped in understanding the mechanism underlying the interactions between Ssa Ab/Bb and 7S/11S. Furthermore, these results highlighted the theoretical fundamentals for the future applications of composite systems as surfactants in the food industry.

Probing the interaction of new and biologically active Pd(II) complex with DNA/BSA via joint experimental and computational studies along with thermodynamic, NLO, FMO and NBO analysis

Treatment with transition metal complexes is an efficient method to fight with cancer. Therefore, a new transition metal complex formulated as [Pd(1, 3-pn)(acac)]Cl (pn and acac stand for propylendiamine and acetylacetonate, respectively) was synthesized and analyzed using ¹H NMR, Fourier transform infrared, electronic absorption spectroscopy techniques as well as elemental analysis and conductivity measurement. The geometry optimization, frontier molecular orbital (FMO) analysis, molecular electrostatic potential (MEP), natural bond orbital (NBO) analysis and nonlinear optical (NLO) property were accomplished by density functional theory (DFT) at B3LYP level with 6-311G(d,p)/aug-cc-pVTZ-PP basis set. Preliminary determination of antitumor activity and lipophilicity of this metal complex was performed experimentally and the promising results were obtained. This encouraged us to study the interaction and binding mode/modes of this complex with DNA as the primary receptor for the chemotropic drugs and BSA as the transporter protein in the circulatory system. For this reason, the binding of newly made complex was assessed in-vitro under physiological state using experimental and in-silico molecular modeling studies. So, the CT-DNA binding study of this complex was explored using spectrofluorometric as well as spectrophotometric techniques, viscosity and gel electrophoresis experiments. Furthermore, fluorescence, UV-Vis, F[Formula: see text]rster resonance energy transfer and circular dichroism studies were carried out for BSA binding. The experimental and computational interaction studies showed that [Pd(1, 3-pn)(acac)]Cl complex binds to the minor groove of CT-DNA and interacts with BSA by van der Waals forces and hydrogen bond.

In vitro anticancer and antibacterial activates of the yttrium(III) complex and its nano-carriers toward DNA cleavage and biological interactions with DNA and BSA; An experimental and computational studie

OBJECTIVES

In this research, the biological properties of the yttrium (III) (Y) complex, with 2,9-dimethyl- 1,10-phenanthroline (Me₂Phen) ligand, were examined for in vitro fish DNA (FS-DNA)/ bovine serum albumin (BSA) interactions, DNA-cleavage, anticancer and antibacterial activities.

METHODS

Multi-spectrophotometric techniques and computational calculations were used for the interaction studies of the BSA and FS-DNA with the Y-complex. Absorption and fluorescence spectroscopy methods were used to define thermodynamic parameters, the binding constants (K_b), and the probable binding mechanism. Also, the DFT (density functional theory) study and molecular docking calculation of the Y-complex were done. Besides, the nanocarriers of Y-complex (lipid nanoencapsulation (LNEP) and the starch nanoencapsulation (SNEP)), as active anticancer candidates, were prepared. Finally, DNA-cleavage, anticancer, and antibacterial activities of this complex were investigated.

RESULTS

The absorption and fluorescence measurements were exhibited that the Y-complex has a high binding affinity to FS-DNA and BSA through a static mechanism. The negative thermodynamic parameter values for both DNA/BSA binding were confirmed that the hydrogen bonds and van der Waals forces played an essential role in the spontaneous bonding procedure. The site marker competitive studies for BSA confirmed that the Y-complex bonds to the sub-domain IB of protein (site III) on BSA, which was entirely agreement by docking calculation. The complex has displayed efficient DNA cleavage, antifungal and antibacterial activities. The anticancer activity of the Y-complex and its starch/lipid nano-encapsulated was carried out in cancer cell lines, which exposed considerably high activity.

CONCLUSIONS

Thus, Y-complex can be transported professionally through BSA in the blood and bonds in the groove of DNA. Base on biological applications of the Y-complex, it can be concluded that this complex and its nanocarriers can suggest as novel anticancer and antibacterial candidates.

A binuclear iron(III) complex of 5,5'-dimethyl-2,2'-bipyridine as cytotoxic agent

The binuclear iron(III) complex (1), namely, {[Fe(5,5'-dmbpy)₂(OH₂₎]₂(µ-O)}(NO₃)₄ with a distorted octahedral coordination, formed by four nitrogen and two oxygen atoms, was previously reported by our team. In this study the DNA-binding and cytotoxicity evaluation for target complex were studied. The results indicated strong cytotoxicity activity against A549 cells comparable to cisplatin values. The binding interaction between complex 1 and FS-DNA was investigated by UV-Vis, fluorescence spectroscopy, and gel electrophoresis at physiological pH (7.2). The DNA binding investigation has shown groove binding interactions with complex 1, therefore the hydrogen binding plays an important role in the interaction of DNA with complex 1. The calculated thermodynamic parameters (ΔH°, ΔS° and ΔG°) show that hydrogen bonding and Vander-Waals forces have an important function in Fe(III) complex-DNA interaction. Moreover, DNA cleavage was studied using agarose gel electrophoresis. Viscosity measurements illustrated that relative viscosity of DNA was unchanged with the adding concentrations of Fe(III) complex. Molecular docking simulation results confirmed the spectroscopic and viscosity titration outcomes.

Interaction between soyasaponin and soy β-conglycinin or glycinin: Air-water interfacial behavior and foaming property of their mixtures

The interaction between soyasaponin and soy β-conglycinin (7S) or glycinin (11S), adsorption of their mixtures at air-water interface, and foaming properties of the mixed system were investigated in this study. Fluorescence spectroscopy results showed that there was a weak binding of soyasaponin with 7S or 11S in bulk solutions, leading to the conformational changes of protein by nonspecific hydrophobic interactions. Dynamic surface properties of soyasaponin-7S/11S mixtures indicated that the composite layers formed via their weak interactions due to the synergy of reducing surface tension and the plateau of elasticity at the interface. Most mixtures represented high foam forming ability and stability except 0.2 % soyasaponin mixture, which could be a consequence that the surface behavior was dominated by soyasaponin under this concentration, and low surface elasticity lead to a less stable interfacial film. Overall, foamability of soyasaponin-7S mixtures were better than 11S ones. All data of this work was helpful to understand air-water behaviors of soyasaponin-7S/11S mixtures. This mixed system has shown good potential for further foam related industrial applications.

Parent and nano-encapsulated ytterbium(iii) complex toward binding with biological macromolecules, in vitro cytotoxicity, cleavage and antimicrobial activity studies

To determine the chemotherapeutic and pharmacokinetic aspects of an ytterbium complex containing 2,9-dimethyl-1,10-phenanthroline (Me₂Phen), in vitro binding studies were carried out with FS-DNA/BSA by employing multiple biophysical methods and a molecular modeling study. There are different techniques including absorption spectroscopy, fluorescence spectroscopy, circular dichroism studies, viscosity experiments (only in the case of DNA), and competitive experiments used to determine the interaction mode between DNA/BSA and the ytterbium-complex. The results showed that the Yb-complex exhibited a high propensity for the interaction of BSA and DNA via hydrophobic interactions and van der Waals forces. Further, a competitive examination and docking study showed that the interaction site of the ytterbium complex on BSA is site III. The results of docking calculations for DNA/BSA were in good agreement with experimental findings. The complex displays efficient DNA cleavage in the presence of hydrogen peroxide. Moreover, antimicrobial studies of different bacteria and fungi indicated its promising antibacterial activity. In vitro cytotoxicity studies of the Yb-complex, starch nano-encapsulated, and lipid nano-encapsulated were carried out in MCF-7 and A-549 cell lines, which revealed significantly good activity. The results of anticancer activity studies showed that the cytotoxic activity of the Yb-complex was increased when encapsulated with nanocarriers. Based on biological applications of the Yb-complex, it can be concluded that this complex and its nanocarriers can act as novel anticancer and antimicrobial candidates.

The biological applications of Yb-complexes including anticancer, antimicrobial and DNA cleavage ability, and their interaction with FS-DNA and BSA were examined.

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.