Publications by authors named "Nahid Shahabadi"

95 Publications

Selenium nanoparticles: Synthesis, cytotoxicity, antioxidant activity and interaction studies with ct-DNA and HSA, HHb and Cyt c serum proteins.

Biotechnol Rep (Amst) 2021 Jun 15;30:e00615. Epub 2021 Apr 15.

Center of Medical Biology Research, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.

The aim of this study was the synthesis of selenium nanoparticles (SeNPs) employing vitamin C as a biocompatible and low toxic reducing agent. The synthesized selenium nanoparticles were characterized by using UV-vis, FT-IR, SEM-EDX, TEM, DLS, and zeta potential measurements. The results of the DPPH free radical scavenging assay demonstrate that this synthesized nano-selenium has strong potentials to scavenge the free radicals and cytotoxicity against MCF-7 and Raji Burkitt's lymphoma cancer cell lines. The interaction of calf thymus DNA (ct-DNA) with SeNPs indicated that the anticancer activity might be associated with the DNA-binding properties of nano-selenium. Finally, it was found that the synthesized nano-selenium can bind to the most important blood proteins such as human serum albumin (HSA), human hemoglobin (HHb), and Cytochrome c (Cyt c). The results showed that the secondary structure of these proteins remains unchanged, suggesting that the synthesized nano-selenium could be employed as a carrier in the drug delivery system without any cytotoxicity effect.
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http://dx.doi.org/10.1016/j.btre.2021.e00615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080047PMC
June 2021

Interaction of human hemoglobin (HHb) and cytochrome c (Cyt c) with biogenic chloroxine-conjugated silver nanoflowers: spectroscopic and molecular docking approaches.

J Biomol Struct Dyn 2021 Apr 30:1-12. Epub 2021 Apr 30.

Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.

In this research, the biological activity of the antibacterial drug Chloroxine-conjugated biogenic AgNPs (COX-AgNPs) was investigated in simulated physiological conditions (pH = 7.40). Different spectroscopic methods such as UV-visible, fluorescence, and circular dichroism spectroscopic and docking simulation were employed to evaluate the structural changes in the most important blood proteins (human hemoglobin (HHb) and Cytochrome c (Cyt c)) in the presence of COX-AgNPs. The results showed that the COX-AgNPs can bind to HHb and Cyt c and the secondary structure of these proteins remains unchanged, which is crucial in providing insights into the side effects of newly synthesized drugs on their carriers.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1919555DOI Listing
April 2021

Insight into the binding mechanism of macrolide antibiotic; erythromycin to calf thymus DNA by multispectroscopic and computational approaches.

J Biomol Struct Dyn 2021 Feb 2:1-12. Epub 2021 Feb 2.

Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.

In the present study, the interactions between Erythromycin drug and calf thymus deoxyribonucleic acid (ct-DNA) were explored by multi spectroscopic techniques (UV-Visible, fluorescence, circular dichroism spectroscopies), viscosity, molecular docking simulation, and atomic force microscopy (AFM). In addition, the values of binding constant were calculated by the UV-Visible and fluorescence spectroscopy. Competitive fluorescence study with methylene blue (MB), acridine orange (AO), and Hoechst 33258 were indicated that the Erythromycin drug could displace the DNA-bound Hoechst, which displays the strong competition of Erythromycin with Hoechst to interact with the groove binding site of DNA. In addition, the observed complexes in AFM analysis comprise the chains of ct-DNA and Erythromycin with an average size of 314.05 nm. The results of thermodynamic parameter calculations (ΔS° = -332.103 ± 14 J mol and ΔH° = -115.839 ± 0.02 kJ mol) approved the critical role of van der Waals forces and hydrogen bonds in the complexation of Erythromycin-DNA. Fluorescence spectroscopy results demonstrate the existence of a static enhancement mechanism in the interaction of Erythromycin-DNA. According to the obtained results, Erythromycin drug interacts with the major groove of ct-DNA. These consequences were further supported by the molecular docking study, and it could be determined that DNA-Erythromycin docked model was in a rough correlation with our experimental results.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1877821DOI Listing
February 2021

Multispectroscopic and molecular docking studies on DNA binding of guaifenesin drug.

Nucleosides Nucleotides Nucleic Acids 2021 19;40(3):317-335. Epub 2021 Jan 19.

Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran.

The interaction mechanism of guaifenesin drug; ()-3-(2-methoxyphenoxy)propane-1,2-diol; and calf thymus DNA was characterized by multiple spectroscopic and molecular docking approaches. The changes in drug electronic absorption with increasing DNA concentration and also the observed significant quenching of guaifenesin emission in the presence of DNA proved the complex formation between guaifenesin and DNA during the interactions. Both the binding constant and thermodynamic parameters for the interaction have been calculated in 283, 298, and 310 K at pH 7.4. The results  = 17.87 kJ/mol and  = 143.31 J/mol.K confirmed the role of hydrophobic force in the guaifenesin-DNA interaction. Circular dichroism study showed that guaifenesin causes decrease in the negative band of CT-DNA and at the same time the positive band increases which indicated the transition of DNA conformation from B to A. KI quenching experiment specifies that guaifenesin binds to DNA via nonintercalative mode. The competitive studies based on known Hoechst 33258 and methylene blue probes proved the groove binding mode in guaifenesin-DNA adduct. Further, full agreement of molecular docking simulation with the experimental results of binding constant and interaction mode, support high accuracy of the results.
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http://dx.doi.org/10.1080/15257770.2021.1872793DOI Listing
June 2021

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

J Biomol Struct Dyn 2020 Dec 17:1-15. Epub 2020 Dec 17.

Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran.

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 [CuCl(ZNS)(Phen)EtOH].HO can bind to the groove site of DNA. The calculated thermodynamic parameters, ΔS° = +201.15 J molK and ΔH° = +41.32 kJ mol 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 [CuCl(ZNS)(Phen)EtOH].HO against B92 cancer cell lines showed better activity in Cu(II) complex in comparison to free ZNS. Therefore, [CuCl(ZNS)(Phen)EtOH].HO can open a new horizon in the treatment of glioma cancer by ZNS metallodrugs.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1861979DOI Listing
December 2020

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

J Biomol Struct Dyn 2020 Dec 4:1-13. Epub 2020 Dec 4.

Phamaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.

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)(MeOH)], at physiological pH has been investigated by multi-spectroscopic techniques and molecular docking. Zinc-naproxen complex displays significant binding property to the CT-DNA ( = 0.2  10 L.mol). 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 and bacteria revealed the high antimicrobial activity of the complex.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1854858DOI Listing
December 2020

Binding Studies of AICAR and Human Serum Albumin by Spectroscopic, Theoretical, and Computational Methodologies.

Molecules 2020 Nov 19;25(22). Epub 2020 Nov 19.

Department of Chemistry and Physics, Louisiana State University, Shreveport, LA 71115, USA.

The interactions of small molecule drugs with plasma serum albumin are important because of the influence of such interactions on the pharmacokinetics of these therapeutic agents. 5-Aminoimidazole-4-carboxamide ribonucleoside (AICAR) is one such drug candidate that has recently gained attention for its promising clinical applications as an anti-cancer agent. This study sheds light upon key aspects of AICAR's pharmacokinetics, which are not well understood. We performed in-depth experimental and computational binding analyses of AICAR with human serum albumin (HSA) under simulated biochemical conditions, using ligand-dependent fluorescence sensitivity of HSA. This allowed us to characterize the strength and modes of binding, mechanism of fluorescence quenching, validation of FRET, and intermolecular interactions for the AICAR-HSA complexes. We determined that AICAR and HSA form two stable low-energy complexes, leading to conformational changes and quenching of protein fluorescence. Stern-Volmer analysis of the fluorescence data also revealed a collision-independent static mechanism for fluorescence quenching upon formation of the AICAR-HSA complex. Ligand-competitive displacement experiments, using known site-specific ligands for HSA's binding sites (I, II, and III) suggest that AICAR is capable of binding to both HSA site I (warfarin binding site, subdomain IIA) and site II (flufenamic acid binding site, subdomain IIIA). Computational molecular docking experiments corroborated these site-competitive experiments, revealing key hydrogen bonding interactions involved in stabilization of both AICAR-HSA complexes, reaffirming that AICAR binds to both site I and site II.
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http://dx.doi.org/10.3390/molecules25225410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7699360PMC
November 2020

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

J Biomol Struct Dyn 2020 Sep 1:1-13. Epub 2020 Sep 1.

Substance Abuse Prevention Research Center, University of Medical Sciences, Kermanshah, Iran.

In this study, an effective nano-drug delivery system was prepared by the co-precipitation method via two steps; the preparation of FeO magnetic nanoparticles and its surface modification with layered double hydroxide (LDH) and loading lamivudine on this nanocarrier ([email protected]@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%. , drug release investigations showed a controlled and pH-dependent lamivudine release over 300 min. The cytotoxic activity of [email protected]@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 [email protected]@Lamivudine NPs significantly inhibited the proliferation of Mel-Rm and A-549 cells in a dose-dependent manner. The influences of [email protected]@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 [email protected]@Lamivudine and indicate that they may be a cost-effective substitute in the treatment of lung and skin cancer.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1812431DOI Listing
September 2020

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

J Biomol Struct Dyn 2020 Aug 14:1-8. Epub 2020 Aug 14.

Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.

In this study, the interaction of [email protected]@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 [email protected]@L-Dopa NPs enforced some conformational alterations within HSA. The fluorescence spectroscopy analysis indicated that by enhancing temperature, the Stern-Volmer quenching constant (K) was decreased, which is relevant to a static quenching mechanism. The binding constant (K) was 7.07 × 10 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 [email protected]@L-Dopa NPs. Displacement studies successfully carried out using the Warfarin and Ibuprofen have predicted that the binding of [email protected]@L-Dopa NPs to HSA is situated at site II (subdomain IIIA).Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1806929DOI Listing
August 2020

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

Nucleosides Nucleotides Nucleic Acids 2020 9;39(8):1122-1133. Epub 2020 Jul 9.

Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.

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 × 10 M 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 (Δ) and entropy change (Δ) showed that the acting forces between didanosine and ct-DNA mainly included hydrophobic interactions.
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http://dx.doi.org/10.1080/15257770.2020.1780435DOI Listing
January 2021

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

J Biomol Struct Dyn 2020 Jun 26:1-15. Epub 2020 Jun 26.

Faculty of Chemistry, K.N. Toosi University of Technology, Tehran, Iran.

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 [SnMeCl(Mephen)] 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 [SnMeCl(Mephen)] 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.
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http://dx.doi.org/10.1080/07391102.2020.1784793DOI Listing
June 2020

spectroscopic investigation of groove binding interaction of [email protected]@L-Dopa with calf thymus DNA.

Nucleosides Nucleotides Nucleic Acids 2020 28;39(7):1020-1035. Epub 2020 Apr 28.

Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.

The principal goal of this study is to evaluate the interaction of [email protected]@L-Dopa and [email protected] nanoparticles with calf thymus DNA. The magnetic nanoparticles were previously prepared by a chemical co-precipitation method, and the surface of the FeO 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 [email protected]@L-Dopa and [email protected] nanoparticles with CT-DNA was studied using, UV-Visible spectroscopy, viscosity, circular dichroism (CD), and fluorescence spectroscopy techniques. The results of investigations demonstrated that [email protected]@L-Dopa and [email protected] nanoparticles have interacted via minor groove binding and intercalated to CT-DNA, respectively.
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http://dx.doi.org/10.1080/15257770.2020.1740929DOI Listing
January 2021

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.

Spectrochim Acta A Mol Biomol Spectrosc 2020 Jul 19;235:118280. Epub 2020 Mar 19.

Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.

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(PPh)(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 10 M, which is in keeping with both groove binders and intercalators. The thermodynamic parameters, ΔS = -200.31 ± 0.08 cal/mol·K and ΔH = -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.
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http://dx.doi.org/10.1016/j.saa.2020.118280DOI Listing
July 2020

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

J Biomol Struct Dyn 2021 Mar 19;39(5):1681-1687. Epub 2020 Mar 19.

Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.

In an attempt to describe how low-energy electrons (LEEs) damage the polypeptide chain at disulfide bridges, 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.
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http://dx.doi.org/10.1080/07391102.2020.1740788DOI Listing
March 2021

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

Spectrochim Acta A Mol Biomol Spectrosc 2020 Apr 10;230:118042. Epub 2020 Jan 10.

Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.

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.
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http://dx.doi.org/10.1016/j.saa.2020.118042DOI Listing
April 2020

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

Ultrason Sonochem 2019 Dec 12;59:104729. Epub 2019 Aug 12.

Department of Chemistry, Faculty of Sciences, Tarbiat Modares University, P.O. Box 14155-4838, Tehran, Islamic Republic of Iran. Electronic address:

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 CO capture compounds. Compared with ultrasound process, the as-prepared daughter frameworks showed enhanced CO 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 CO sorption in Zn-TMU by a SALE method.
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http://dx.doi.org/10.1016/j.ultsonch.2019.104729DOI Listing
December 2019

Design, synthesis and DNA interaction studies of new fluorescent platinum complex containing anti-HIV drug didanosine.

J Biomol Struct Dyn 2020 Jul 6;38(10):2837-2848. Epub 2019 Sep 6.

Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.

Forming coordination complexes with nucleoside analogues may be helpful in studying anti-tumour activity of them. Therefore, to improve the clinical efficacy of nucleoside analogue and design new ones, a new fluorescent platinum (Pt) complex with anti-human immunodeficiency virus drug didanosine (ddI); K[PtCl(OCH)(ddI)]; was synthesized and characterized. The ultraviolet-visible (UV-vis) spectroscopy, infrared, thermogravimetric analysis, mass assignments and elemental analysis confirmed the preparation of the complex. The molecular ion peaks seen at the positive mass spectrum of Pt complex confirm coordination of the drug to metal centre. The interaction of this complex with calf thymus DNA (ct-DNA) was studied using several spectroscopic techniques such as UV absorption, fluorescence spectroscopy and dynamic viscosity measurements. Hyperchromism of the band in the UV-vis spectra and the intrinsic binding constant (0.56 ± 0.25) × 10 M, decreasing in Hoechst-DNA fluorescence by adding Pt complex concentration and also relatively small changes in DNA viscosity indicated that this complex could interact as a groove-binder. According to the UV spectra and the fluorescence quenching of the complex in our case seems to be primarily caused by complex formation between the Pt complex and DNA. The thermodynamic parameters showed that hydrogen bond and van der Waals interactions play main roles in the binding of Pt complex to ct-DNA. The free energy values are negative, showing the spontaneity of the Pt complex-DNA binding. The docking simulation was performed and the results confirm a preference of groove site of synthesized complex on DNA helix. The knowledge gained from this study will be helpful to further understand the DNA binding mechanism and can also provide much fruitful information for designing a new type of anti-cancer drugs.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2019.1658643DOI Listing
July 2020

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

Nucleosides Nucleotides Nucleic Acids 2019 7;38(11):901-919. Epub 2019 Jun 7.

Kermanshah University of Medical Science, Pharmacy College , Iran.

The interaction of the [Mn(mef)(phen)HO] 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 × 10 Lmol. 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.
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http://dx.doi.org/10.1080/15257770.2019.1625379DOI Listing
October 2019

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

Nucleosides Nucleotides Nucleic Acids 2019 14;38(10):732-751. Epub 2019 May 14.

a Department of Inorganic Chemistry, Faculty of Chemistry, Razi University , Kermanshah , Iran.

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 × 10 L mol. 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.
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http://dx.doi.org/10.1080/15257770.2019.1594892DOI Listing
September 2019

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

Nucleosides Nucleotides Nucleic Acids 2019 11;38(2):157-182. Epub 2019 Mar 11.

a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran.

The interaction of SnMeCl(bubpy)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 SnMeCl(bubpy) 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 PO 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 SnMeCl(bubpy) 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.
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http://dx.doi.org/10.1080/15257770.2018.1506885DOI Listing
May 2019

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

Spectrochim Acta A Mol Biomol Spectrosc 2019 Aug 22;219:195-201. Epub 2019 Apr 22.

Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran.

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 ΔH = -122.76 ± 0.07 kJ/mol and ΔS = -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).
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http://dx.doi.org/10.1016/j.saa.2019.04.059DOI Listing
August 2019

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

Mater Sci Eng C Mater Biol Appl 2019 Aug 4;101:472-486. Epub 2019 Apr 4.

Medical Biology Research Center (MBRC), University of Medical Sciences, Kermanshah, Iran.

In this study, an efficient drug delivery system composed of FeO, CaAl layered double hydroxide (LDH) and l-Dopa has been synthesized through hydrogen bonds between l-Dopa and CaAl-LDH encapsulated FeO nanoparticles ([email protected]@l-Dopa). The structural features of [email protected]@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 [email protected]@l-Dopa were investigated against Mel-Rm Cells Melanoma (NCIt: C3224) using LDH colorimetric assay and differential staining cell death assay. The results showed [email protected]@l-Dopa with a lower concentration of l-Dopa, illustrate a higher cytotoxicity and anticancer activity.
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http://dx.doi.org/10.1016/j.msec.2019.04.004DOI Listing
August 2019

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

Nucleosides Nucleotides Nucleic Acids 2019 3;38(9):680-699. Epub 2019 Apr 3.

a Department of Inorganic chemistry Faculty of Chemistry , Razi University , Kermanshah , Iran.

A new copper(II) complex, [Cu(pse)(phen)Cl]; 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 × 10 L mol. 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).
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http://dx.doi.org/10.1080/15257770.2019.1599909DOI Listing
September 2019

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

Nucleosides Nucleotides Nucleic Acids 2019 1;38(6):428-447. Epub 2019 Apr 1.

a Department of Inorganic chemistry Faculty of Chemistry , Razi University , Kermanshah , Iran.

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. The obtained theoretical results were in good agreement with those obtained from experimental studies.
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http://dx.doi.org/10.1080/15257770.2018.1562071DOI Listing
June 2019

A novel sensitive laccase biosensor using gold nanoparticles and poly L-arginine to detect catechol in natural water.

Biotechnol Appl Biochem 2019 Jul 5;66(4):502-509. Epub 2019 Apr 5.

Faculty of Chemistry, Razi University, Kermanshah, Iran.

In this study, the simple, green, and fast layer-by-layer modification of the glassy carbon electrode was mainly performed by electrodeposition of gold nanoparticles and then, poly-l-arginine, and finally, laccase was covalently bonded to poly-l-arginine using glutaraldehyde. This type of fabrication is used for the first time for catechol detection, which provides a bioelectrocatalytic cycle for electron transport in the presence of laccase that results in sensitive and fast detection of catechol. The scanning electron microscopy, Fourier-transform infrared spectroscopy, and electrochemical studies were performed to confirm successful immobilization of the enzyme. The biosensor response was linear in a wide range of catechol trace concentrations, 24.90-274.00 nM, with the detection limit of 18.00 nM. Values of K , α, n, and K for the immobilized enzyme were calculated to be 1.25 × 10  µM, 0.56, 3.19, and 0.28 Sec , respectively. It was examined in real sample successfully confirming it is capable of measuring catechol in natural water.
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http://dx.doi.org/10.1002/bab.1746DOI Listing
July 2019

New water-soluble [email protected] magnetic nanoparticles functionalized with levetiracetam drug for adsorption of essential biomolecules by case studies of DNA and HSA.

J Biomol Struct Dyn 2020 01 19;38(1):283-294. Epub 2019 Feb 19.

Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.

Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2019.1569557DOI Listing
January 2020

Nontoxic silver nanocluster-induced folding, fibrillation, and aggregation of blood plasma proteins.

Int J Biol Macromol 2018 Nov 29;119:838-848. Epub 2018 Jul 29.

Research Center of Oils and Fats, Kermanshah University of Medical Sciences, Kermanshah, Iran. Electronic address:

In recent years, concerns have been raised considering the potential risks of nanocluster (NC) for the environment and human health. Since the blood circulation system is probably the first entry route of NC into the human body, adsorption of blood proteins on NC may change cellular responses, including cellular uptake efficiency, bio distribution patterns, and nanotoxicity profiles, besides other biological effects. Therefore, the interaction of NCs with proteins and the cellular implications can be therapeutically of great importance. Adsorption of human blood proteins on NCs has been methodically investigated. In the present study, the first analysis of fibrillation was conducted between MBI-AgNCs and human serum (a complex biofluid). AgNCs were prepared by coating with 2-mercaptobenzimidazole. Then, interactions with human blood proteins, such as immunoglobulin, albumin, and insulin were investigated using various experimental approaches. Upon protein association, the fluorescence of proteins significantly decreased, accompanied by a blue shift in the AgNCs-human serum albumin (HSA) system and a red shift in the AgNCs-insulin/γ-globulin. Concomitantly, circular dichroism spectroscopy and atomic force microscopy were employed to investigate the effects of protein binding to NCs. We found that AgNCs induced γ-globulin aggregation. HSA at the AgNC surface was partially unfolded and could promote protein self-assembly into amyloid fibrils, while the surface morphology remained unchanged after insulin incubation. The atomic force microscopy (AFM) data and the ThT and CR analysis of the proteins, as well as circular dichroism (CD) and fluorescence findings, support the use of AgNCs as an indicator for monitoring the progress of HSA fibrillogenesis. Additionally, cytotoxicity assays were used to ensure the biocompatibility of nanoparticles within the applicable limits.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.07.177DOI Listing
November 2018

DNA binding and cytotoxicity studies of magnetic nanofluid containing antiviral drug oseltamivir.

J Biomol Struct Dyn 2019 07 5;37(11):2980-2988. Epub 2018 Dec 5.

b Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences , Kermanshah , Iran.

In this work, the possibility of preparing a nanoparticle with improved treatment properties was investigated. In this regard, synthesis, characterization, in vitro cytotoxicity and DNA binding of [email protected]/oseltamivir magnetic nanoparticles (MNPs) were investigated. FeO nanoparticles were synthesized via chemical co-precipitation and coated by oleate bilayers. Then, [email protected] MNPs were functionalized with an antiviral drug (oseltamivir), for better biological applications. The MNPs were subsequently characterized by zeta sizer and Zeta potential measurements, Fourier transform infrared (FT-IR) spectroscopy, vibrating sample magnetometer (VSM) and transmission electron microscopy (TEM) analyses. The TEM image demonstrated that average sizes of [email protected]/oseltamivir MNPs were about 8 nm. The in vitro cytotoxicity of [email protected]/oseltamivir MNPs was studied against cancer cell lines (MCF-7 and MDA-MB-231) and compared with oseltamivir drug. The results illustrated that [email protected]/oseltamivir magnetic nanoparticles have better antiproliferative effects on the mentioned cell lines as compared with oseltamivir. Also, in vitro DNA binding studies were done by UV-Vis, circular dichroism, and Fluorescence spectroscopy. The results indicated that [email protected]/oseltamivir MNPs bound to DNA via groove binding. Moreover, this magnetic nanofluid has potential for magnetic hyperthermia therapy due to magnetic core of its nanoparticles. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2018.1502685DOI Listing
July 2019

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

Nucleosides Nucleotides Nucleic Acids 2018 Mar 21;37(3):147-168. Epub 2018 Feb 21.

a Inorganic Chemistry Department, Faculty of Chemistry , Razi University , Kermanshah , Iran.

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 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.
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http://dx.doi.org/10.1080/15257770.2018.1438617DOI Listing
March 2018

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.

Nucleosides Nucleotides Nucleic Acids 2018 20;37(3):125-146. Epub 2018 Feb 20.

Medical Biology Research Center, Arak University of Medical Sciences, Arak, Iran.

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 = (1.00 ± 0.2) × 10 M) 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.
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http://dx.doi.org/10.1080/15257770.2017.1400048DOI Listing
February 2018