Interaction of water soluble phthalocyanine compounds with parallel and hybrid G-quadruplex DNA molecules

Aydin, Fadime; Bağda, Esra; Bağda, Efkan; Durmuş, Mahmut

doi:10.1016/j.poly.2023.116413

Cited by 3 publications

(2 citation statements)

References 41 publications

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“…It is generally thought that small molecules disrupt the double helix structure of DNA. Small molecules in the DNA structure cause a significant hypochromic effect (usually more than 35 %) and a redshift of the peak position (15 nm) [20] . In contrast, binding of small molecules to the DNA groove causes a hypochromic effect with little or no shift in the absorption band [21] .…”

Section: Resultsmentioning

confidence: 99%

“…Small molecules in the DNA structure cause a significant hypochromic effect (usually more than 35 %) and a redshift of the peak position (15 nm). [20] In contrast, binding of small molecules to the DNA groove causes a hypochromic effect with little or no shift in the absorption band. [21] In this part of our bioanalytical studies, the absorption spectra of the solutions prepared at different concentrations were examined and the interaction of compound 2 with FSdsDNA was investigated.…”

Section: Dna Binding Properties Of Compoundmentioning

confidence: 99%

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Synthesis, DNA Binding Properties, Molecular Docking and ADME Studies of Schiff Base Compound Containing Pyridine‐Propargyl Group

Güngör

2023

Chemistry & Biodiversity

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The structure of the pyridine‐based Schiff base compound containing the propargyl group was characterized by NMR spectroscopy. Binding of compound 2 with double‐stranded fish sperm DNA (Fsds‐DNA) was investigated using viscosity measurement studies and UV‐Vis and fluorescence spectral techniques. Binding of compound 2 with Fsds‐DNA results in minor hypochromism with no change in absorption maxima and fluorescence quenching with almost no shift in emission maxima, which can be attributed to the groove‐binding mode of the interaction. The binding constant was found to be 4.7 x 104 M‐1. The Fsds‐DNA viscosity measurement, KI quenching and NaCl quenching studies and the competitive interaction between compound 2 and ethidium bromide with DNA confirm the proposed binding mode. In addition, interactions between compound 2 and the DNA double helix were analysed by molecular docking study in order to determine the binding mode and binding affinity. As a result of molecular docking, the binding affinity of the 2‐DNA complex, which has the most stable conformation ‐8.10 kcal/mol and it is located in its minor groove. In addition, molecular docking and ADME studies for compound 2 were also performed.

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Section: Resultsmentioning

confidence: 99%

Section: Dna Binding Properties Of Compoundmentioning

confidence: 99%

Synthesis, DNA Binding Properties, Molecular Docking and ADME Studies of Schiff Base Compound Containing Pyridine‐Propargyl Group

Güngör

2023

Chemistry & Biodiversity

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Role of Secondary Structure and Time‐Dependent Binding on Disruption of Phthalocyanine Aggregates by Guanine‐Rich Nucleic Acids

Windle,

Rennie,

Edkins

et al. 2024

Chemistry A European J

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Phthalocyanines are versatile photodynamic therapy agents whose biological activity depends on their aggregation state, which is expected to be influenced by binding to biomolecules. Here, guanine‐rich nucleic acid binding of a water‐soluble cationic, regiopure C4h zinc phthalocyanine bearing four triethylene glycol methyl ether and four N‐methyl‐4‐pyridinium substituents (1) is reported. In contrast to double‐stranded DNA, guanine systems GpG, (GG)10, poly(G) and quadruplex DNA are shown to effectively disrupt phthalocyanine aggregates in buffered solution. This process is accompanied by evolution of the Q‐band absorbance and enhanced emission. Increasing the sequence length from GpG to (GG)10 increases the binding and confirms the importance of multiple binding interactions. Enhanced binding in the presence of KCl suggests the importance of nucleobase hydrogen‐bonded mosaics in phthalocyanine binding. Notably, the (GT)10 sequence is even more effective than quadruplex and pure guanine systems at disrupting the aggregates of 1. Significant time‐dependent binding of 1 with poly(G) reveals biexponential binding over minutes and hours, which is linked to local conformations of poly(G) that accommodate monomers of 1 over time. The study highlights the ability of biomacromolecules to disrupt phthalocyanines aggregates over time, which is an important consideration when rationalizing photoactivity of photosensitizers in‐vivo.

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Thermodynamic and structural investigation of the interaction of quaternized 2,3‐octakis‐[(2‐mercaptopyridine)phthalocyaninato] copper (II) sulfate (CuPc) with parallel and hybrid type G‐quadruplex

Şahin,

Bağda,

Göktuğ Temiz

et al. 2023

J of Molecular Recognition

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G‐quadruplexes are important drug targets and get attention due to their existence in telomere, ribosomal DNA, promoter regions of some oncogenes, and the untranslated regions of mRNA. Due to the biological roles of G‐quadruplexes, investigating of the G‐quadruplex–small molecule interaction is essential. The primary motivation for these studies is the possibility of inhibiting cell functions associated with G‐quadruplex sequences by binding with small molecules. Targeting the small molecules to desired tissue with the G‐quadruplex vehicles is the second important goal of the G‐quadruplex–small molecule interaction studies. In the present study, the new peripherally 2‐mercaptopyridine octasubstituted copper(II) phthalocyanine and its quaternized derivative (CuPc) were synthesized and characterized by elemental analysis FT‐IR, UV–Vis, and mass spectra. The excellent solubility of CuPc in water is essential for its transport in the organism. Because of this feature, its affinity toward G‐quadruplex forming aptamers, AS1411, Tel21, and Tel45, was investigated. The UV–Vis spectrophotometric titration data confirmed the prevention of aggregation upon interaction with G‐quadruplex, which is very important for biomedical applications. The CD spectroscopic analyses and binding stoichiometry confirmed the “end stacking” model for interaction of AS1411 with CuPc. The interaction of CuPc caused the equilibrium shift from hybrid conformation to antiparallel conformation for Tel21 and Tel45. The isothermal titration calorimeter (ITC) was used for the determination of thermodynamic parameters. The thermodynamic data of the interaction was fitted well with the one‐site model. The negative values of Gibbs free energy change confirmed the spontaneous nature of the reactions. Besides, the negative values of enthalpy change and entropy change proved that the nature of processes was “enthalpy driven.” The interaction stoichiometry was 2 for AS1411 and Tel21 and 1.5 for Tel45. The binding constants were 1.3(±0.3) × 105, 3.2(±0.4) × 105, and 1.1(±0.3) × 105 M−1, which were at the level of ethidium bromide intercalation binding constant given in the literature. The DNA polymerase stop assay further supported the interaction of CuPc with G‐quadruplex DNA. The experimental results confirm that the CuPc has a potential photosensitizer behaviour for photodynamic therapy.

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Interaction of water soluble phthalocyanine compounds with parallel and hybrid G-quadruplex DNA molecules

Cited by 3 publications

References 41 publications

Synthesis, DNA Binding Properties, Molecular Docking and ADME Studies of Schiff Base Compound Containing Pyridine‐Propargyl Group

Synthesis, DNA Binding Properties, Molecular Docking and ADME Studies of Schiff Base Compound Containing Pyridine‐Propargyl Group

Role of Secondary Structure and Time‐Dependent Binding on Disruption of Phthalocyanine Aggregates by Guanine‐Rich Nucleic Acids

Thermodynamic and structural investigation of the interaction of quaternized 2,3‐octakis‐[(2‐mercaptopyridine)phthalocyaninato] copper (II) sulfate (CuPc) with parallel and hybrid type G‐quadruplex

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