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Shahabadi N, Ghaffari L, Mardani Z, Shiri F. Interaction studies of water-soluble Zn(II) complex with calf thymus DNA using biophysical and molecular docking methods". NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:493-516. [PMID: 37963106 DOI: 10.1080/15257770.2023.2280001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
The binding between a fluorescent water-soluble Zn(II) complex of {2-[N-(2-hydroxyethylammonioethyl) imino methyl] phenol} and calf thymus DNA (ct-DNA) was investigated using spectroscopic techniques. The complex was prepared and identified by FT-IR, and 1H NMR spectroscopies. The significant changes in the absorption and the circular dichroism spectra of ct-DNA in the presence of the Zn(II) complex implied the interaction between the Zn(II) complex and ct-DNA. Upon addition of ct-DNA, the fluorescence emission intensity of the Zn(II) complex was increased and indicated the interaction between the Zn(II) complex and ct-DNA was occurred. The binding constant values (Kb) resulted from fluorescence spectra clearly showed the Zn(II) complex affinity to ct-DNA. The fluorescence studies also approved the static enhancement mechanism in the Zn(II) complex-DNA complexation process. The thermodynamic profile exhibited the exothermic and spontaneous formation of ct-DNA-Zn(II) complex system via hydrogen bonds and van der Waals forces. The competitive fluorescence investigation by methylene blue (MB), and Hoechst 33258 demonstrated that the Zn(II) complex could replace the DNA-bound Hoechst and bind to the minor groove binding site in ct-DNA. The viscosity changes were negligible, representing the Zn(II) complex binding to DNA via the groove binding mode. Molecular docking simulation affirmed that the Zn(II) complex is located in the minor groove of ct-DNA near the DG12, DA17, DA18, and DG16 nucleobases.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Lida Ghaffari
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
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Naik R, Seetharamappa J. In Vitro and Computational Approaches to Untangle the Binding Mechanism of Galangin with Calf Thymus DNA. J Fluoresc 2023; 33:13-24. [PMID: 36209269 DOI: 10.1007/s10895-022-03033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/20/2022] [Indexed: 02/04/2023]
Abstract
Flavonoids have potential applications in the nutraceutical, medicinal, pharmaceutical and cosmetic fields. The binding of flavonoids with DNA could unravel essential information required for the design of novel and effective chemical agents. The present paper describes the interaction of a flavonoid and a potent anticancer drug, galangin (GAL) with calf thymus DNA (ct-DNA) by fluorescence, UV absorption, melting studies, viscosity measurements and molecular docking studies. A hyperchromic effect was noticed in the absorption spectra of ct-DNA in the presence of the GAL system, indicating the presence of a groove mode of binding. Furthermore, GAL persuaded the minor changes in ct-DNA viscosity, indicating a non-intercalative mode of binding. Fluorescence studies revealed that the GAL quenched the fluorescence intensity of ct-DNA-Hoechst, thereby indicating the interaction between GAL and ct-DNA. Fluorescence results obtained at 298, 308 and 318 K revealed that the fluorescence quenching of ct-DNA-Hoechst-GAL occurred through the static quenching mechanism. Thermodynamic parameters for ct-DNA-Hoechst-GAL were computed and suitable conclusions were drawn. The changes noticed in the conformation of ct-DNA upon interaction with GAL were evaluated in terms of molar ellipticity. It indicated a plausible interaction between ct-DNA and GAL. The molecular docking studies also confirmed the groove mode of binding in the ct-DNA-GAL system. Thus, this work helped to unravel the binding mechanism between GAL and ct-DNA.
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Affiliation(s)
- Roopa Naik
- Department of Chemistry, Karnatak University, Dharwad, 580003, Karnataka, India
| | - J Seetharamappa
- Department of Chemistry, Karnatak University, Dharwad, 580003, Karnataka, India.
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Anjomshoa M, Amirheidari B. Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy. Coord Chem Rev 2022; 458:214417. [PMID: 35153301 PMCID: PMC8816526 DOI: 10.1016/j.ccr.2022.214417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/09/2022] [Indexed: 12/25/2022]
Abstract
Despite the extensive and rapid discovery of modern drugs for treatment of cancer, microbial infections, and viral illnesses; these diseases are still among major global health concerns. To take inspiration from natural nucleases and also the therapeutic potential of metallopeptide antibiotics such as the bleomycin family, artificial metallonucleases with the ability of promoting DNA/RNA cleavage and eventually affecting cellular biological processes can be introduced as a new class of therapeutic candidates. Metal complexes can be considered as one of the main categories of artificial metalloscissors, which can prompt nucleic acid strand scission. Accordingly, biologists, inorganic chemists, and medicinal inorganic chemists worldwide have been designing, synthesizing and evaluating the biological properties of metal complexes as artificial metalloscissors. In this review, we try to highlight the recent studies conducted on the nuclease-like metalloscissors and their potential therapeutic applications. Under the light of the concurrent Covid-19 pandemic, the human need for new therapeutics was highlighted much more than ever before. The nuclease-like metalloscissors with the potential of RNA cleavage of invading viral pathogens hence deserve prime attention.
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Shahabadi N, Ghaffari L, Mardani Z, Shiri F. Experimental and Molecular Docking Studies on the Interaction of a Water-Soluble Pd(II) Complex Containing β-Amino Alcohol with Calf Thymus DNA. Biol Trace Elem Res 2022; 200:1988-2000. [PMID: 34218426 DOI: 10.1007/s12011-021-02803-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/18/2021] [Indexed: 02/03/2023]
Abstract
The interaction of water-soluble and fluorescent [Pd (HEAC) Cl2] complex, in which HEAC is 2-((2-((2-hydroxyethyl)amino)ethyl)amino) cyclohexanol, with calf thymus DNA (ct-DNA) has been studied. This study was performed using electronic absorption and fluorescence emission spectroscopies, cyclic voltammetry and circular dichroism analyses, dynamic viscosity measurements, and molecular docking theory. From hypochromic effect observed in ct-DNA absorption spectra, it was found that the Pd(II) complex could form a conjugate with ct-DNA strands through the groove binding mode. The Kb values obtained from fluorescence measurements clearly assert the Pd(II) complex affinity to ct-DNA. The fluorescence quenching of the DNA-Hoechst compound following the successive additions of the Pd(II) complex to the solution revealed that the Pd(II) complex is located in the ct-DNA grooves, and Hoechst molecules have been released into solution; moreover, the resulting measurements from relative viscosity authenticate the Pd(II) complex binding to the grooves. Negative quantities of thermodynamic parameters imply that the Pd(II) complex binds to ct-DNA mainly by the hydrogen bonds and van der Waals forces; also, the Gibbs-free energy changes show the exothermic and spontaneous formation of the Pd(II) complex-DNA system. The electrochemical behavior of the Pd(II) complex in the attendance of ct-DNA was investigated using the cyclic voltammetry method (CV). Several quasi-reversible redox waves were observed along with increasing the anodic/cathodic peak currents, as well as a shift in anodic/cathodic peak potentials. Circular dichroism (CD) observations suggested that the Pd(II)-DNA interaction could alter ct-DNA conformation. The results of molecular modeling confirmed that groove mechanism is followed by the Pd(II) complex to interact with ct-DNA.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.
- Center of Medical Biology Research (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Lida Ghaffari
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
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Chang LL, Yang J, Lai SQ, Liu XR, Yang ZW, Zhao SS. Synthesis, crystal structures and CT-DNA/BSA binding properties of Co(III) and Cu(II) complexes with bipyridine Schiff base ligand. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Caglar S, Altay A, Harurluoglu B, Yeniceri EKK, Caglar B, Şahin O. Synthesis, structural characterization and evaluation of anticancer activity of polymeric silver(I) complexes based on niflumic acid/naproxen and picoline derivatives. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2045586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sema Caglar
- Department of Chemistry, Faculty of Arts and Sciences, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Ahmet Altay
- Department of Chemistry, Faculty of Arts and Sciences, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Betul Harurluoglu
- Department of Chemistry, Institute of Science and Technology, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Esma K. K. Yeniceri
- Department of Chemistry, Institute of Science and Technology, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Bulent Caglar
- Department of Chemistry, Faculty of Arts and Sciences, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Onur Şahin
- Department of Occupational Health and Safety, Faculty of Health Sciences, Sinop University, Sinop, Turkey
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Han Mİ, İnce U, Gündüz MG, Küçükgüzel ŞG. Synthesis, Antimicrobial Evaluation, and Molecular Modeling Studies of New Thiosemicarbazide-Triazole Hybrid Derivatives of (S)-Naproxen. Chem Biodivers 2022; 19:e202100900. [PMID: 35191589 DOI: 10.1002/cbdv.202100900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/21/2022] [Indexed: 11/08/2022]
Abstract
The discovery of new antimicrobial molecules is crucial for combating drug-resistant bacterial and fungal infections that pose a dangerous threat to human health. In the current research, we applied a molecular hybridization approach to synthesize original thiosemicarbazide-triazole derivatives starting from ( S )-Naproxen ( 7a-7k ). After structural characterization using FT-IR, 1 H NMR, 13 C NMR, and HR-MS, the obtained compounds were screened for their antimicrobial activities against Staphylococcus aureus ATCC 29213 , Escherichia coli ATCC 25922 , Candida albicans ATCC 10231 and their isolates, as well. Although all compounds were found to be moderate antimicrobial agents, in general, their antibacterial activities were better than antifungal effects. Among the tested compounds, 7j carrying nitrophenyl group on the thiosemicarbazide functionality represented the best MIC value against S. aureus isolate. Finally, molecular docking studies were performed in the active pocket of S. aureus flavohemoglobin to rationalize the obtained biological data.
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Affiliation(s)
- Muhammed İhsan Han
- Erciyes University: Erciyes Universitesi, Faculty of Pharmacy, ERCİYES ÜNİVERSİTESİ ECZACILIK FAKÜLTESİ, ERCİYES ÜNİVERSİTESİ ECZACILIK FAKÜLTESİ, 38039, TALAS, TURKEY
| | - Ufuk İnce
- Erciyes University: Erciyes Universitesi, Faculty of Pharmacy, ERCİYES ÜNİVERSİTESİ ECZACILIK FAKÜLTESİ, ERCİYES ÜNİVERSİTESİ ECZACILIK FAKÜLTESİ, Türkiye, 38039, TALAS, TURKEY
| | - Miyase Gözde Gündüz
- Hacettepe University: Hacettepe Universitesi, Faculty of Pharmacy, Hacettepe University, Ankara, TURKEY
| | - Ş Güniz Küçükgüzel
- Fenerbahçe University: Fenerbahce Universitesi, Pharmacuitical Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University,, Türkiye, 34668, İSTANBUL, TURKEY
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Shahabadi N, Zendehcheshm S. 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; 40:8913-8924. [PMID: 33928842 DOI: 10.1080/07391102.2021.1919555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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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Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Zendehcheshm
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
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