Development of viscometric methods for studying the interaction of porphyrins with DNA

Barkhudaryan, Vigen G.; Ananyan, Gayane V.

doi:10.1080/07391102.2019.1660217

Cited by 4 publications

(4 citation statements)

References 44 publications

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“…This causes a diminution in the DNA helical twist and an extension of the DNA. Moreover, a molecule can be presumed to bind to deoxyribonucleic acid by intercalation between base pairs if it causes lengthening and unwinding of the deoxyribonucleic acid base pairs [ 72 ]. In this case, the relative viscosity of DNA gradually increases, while the concentration of deoxyribonucleic acid increases.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Assessment of Biomolecular Interactions of Morpholine‐Based Mixed Ligand Cu(II) and Zn(II) Complexes of 2,2′‐Bipyridine as Potential Anticancer and SARS‐CoV‐2 Agents: A Synergistic Experimental and Structure‐Based Virtual Screening

Sakthikumar

Krause

Isamura

2022

Bioinorganic Chemistry and Applications

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A new class of pharmacologically active mixed-ligand complexes (1a-2a) [MII(L)2 (bpy)], where L = 2-(4-morpholinobenzylideneamino)phenol), bpy = 2,2′-bipyridine, MII = Cu (1a), and Zn (2a), were assigned an octahedral geometry by analytical and spectral measurements. Gel electrophoresis showed that complex (1a) demonstrated the complete DNA cleavage mediated by H2O2. The overall DNA-binding constants observed from UV-vis, fluorometric, hydrodynamic, and electrochemical titrations were in the following sequence: (1a) > (2a) > (HL), which suggests that the complexes might intercalate DNA, a possibility that is further supported by the biothermodynamic characteristics. The binding constant results of BSA by electronic absorption and fluorometric titration demonstrate that complex (1a) exhibits the highest binding effectiveness among others, which means that all compounds could interact with BSA through a static approach, additionally supported by FRET measurements. Density FunctionalTheory (DFT) and molecular docking calculations were relied on to unveil the electronic structure, reactivity, and interacting capability of all substances with DNA, BSA, and SARS-CoV-2 main protease (Mpro). These observed binding energies fell within the following ranges: −7.7 to −8.6, −7.2 to −10.2, and −6.7 to −8.2 kcal/mol, respectively. The higher reactivity of the complexes compared to free ligand is supported by the Frontier MolecularOrbital (FMO) theory. The in vitro antibacterial, cytotoxic, and radical scavenging characteristics revealed that complex (1a) has the best biological efficacy compared to others. This is encouraged because all experimental findings are closely correlated with the theoretical measurements.

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Section: Resultsmentioning

confidence: 99%

Comprehensive Assessment of Biomolecular Interactions of Morpholine‐Based Mixed Ligand Cu(II) and Zn(II) Complexes of 2,2′‐Bipyridine as Potential Anticancer and SARS‐CoV‐2 Agents: A Synergistic Experimental and Structure‐Based Virtual Screening

Sakthikumar

Krause

Isamura

2022

Bioinorganic Chemistry and Applications

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“…Moreover, a fully modified PGO formed highly stable duplexes with DNA or RNA even in deionized The present work summarizes possibilities of a viscometry method for studying the conformational changes of DNA at interaction with porphyrins. For elucidating the influence of porphyrin structure by varying the metal center, peripheral substituents and their positions in pyridylic ring on binding mode and intensity of interaction with DNA water soluble cationic meso-tetra-(3N-and 4N-hydroxyethylpyridyl) (Barkhudaryan & Ananyan, 2014, (3N-and 4N-allylpyridyl) (Barkhudaryan & Ananyan, 2017 porphyrins and their metal complexes with Cu and Co were studied via viscometry and UV-vis absorption spectroscopy. It was shown that planar porphyrins interact with DNA by intercalation mode (Figure 1a, b), excepting CuTAllPyP4 which interacts with DNA by partial intercalation mod (Barkhudaryan & Ananyan, 2018).…”

Section: Liangzhen Zheng and Yuguang Mumentioning

confidence: 99%

“…For elucidating the influence of porphyrin structure by varying the metal center, peripheral substituents and their positions in pyridylic ring on binding mode and intensity of interaction with DNA water soluble cationic meso-tetra-(3N-and 4N-hydroxyethylpyridyl) (Barkhudaryan & Ananyan, 2014, (3N-and 4N-allylpyridyl) (Barkhudaryan & Ananyan, 2017 porphyrins and their metal complexes with Cu and Co were studied via viscometry and UV-vis absorption spectroscopy. It was shown that planar porphyrins interact with DNA by intercalation mode (Figure 1a, b), excepting CuTAllPyP4 which interacts with DNA by partial intercalation mod (Barkhudaryan & Ananyan, 2018). Moreover, the planar porphyrins with allylpyridyl peripheral substituents interact with DNA considerably more intensively than with hydroxyethylpyridyl substituents.…”

Section: Liangzhen Zheng and Yuguang Mumentioning

confidence: 99%

Book of Abstracts. Albany 2019: The 20th Conversation

Sarma¹

2019

Journal of Biomolecular Structure and Dynamics

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The aim of structural biology is to explain life processes in terms of macromolecular interactions in the cell. These interactions typically involve more than two partners, and can run up to dozens. A full description will need to characterize all structures on the atomic level, and the way these structures change in the process. Because of the crowded environment of the cell, such characterization is presently (but see below) only possible when the group of interacting molecules (often organized into processive 'molecular machines') is isolated and studied in vitro. While X-ray crystallography has provided structures of a large number of molecular structures, the need for crystals diffracting to high resolution has severely limited the number of supramolecular assemblies and the range of conformers that can be studied with this technique. Single-particle cryo-electron microscopy is about to fill this gap, allowing functional processes to be studied in great detail without imposing restraints on the structures. There are many examples now for this expansion of Structural Biology toward a full characterization of a functional process. Future developments of single-particle cryo-EM include the study of short-lived intermediates in a nonequilibrium system by time-resolved techniques, and the characterization of continuous structural changes using data mining from large ensembles of molecule images. It is very interesting and promising that another technique of cryo-EM, cryo-electron tomography of FIB-milled cell sections, has started to contribute information about processes even within the cellular context. Distinct ribosome states, for instance, have already been identified and localized by subtomogram averaging. With this advance, we get closer to the fulfillment of the most ambitious aim of Structural Biology, the visualization and interpretation of molecular interactions in situ.

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“…Viscosity measurements are one of the most convenient and informative tools for studying liquids of various nature. Viscometry is widely used in analytical chemistry [1]- [3], in the physical chemistry of polymers [4]- [7], biophysics [8] (for example, to study the interaction of Deoxyribonucleic acid (DNA) with porphyrins [9]), in biochemistry [10], in pharmaceutics (for example, to study the nature of the interaction of drugs with low-molecular substances [11], which makes it possible to simulate the effect of drugs on human organism), and to study the fuel characteristics [12], [13].…”

Section: Introductionmentioning

confidence: 99%

The design of viscometer with smartphone controlling

Сулейменов

Mun²,

Kabdushev³

et al. 2022

IJEECS

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New design of a viscometer based on the s tokes viscosity measurement method is proposed. The principle of operation of this viscosimetr is based on the use of ball periodic alternated movement in a horizontally positioned cuvette that filled with the test liquid. The movement appears under the in fluence of a magnetic field that created by two electromagnets. Registration of the ball movement inside the cuvette is carried out using an optoelectronic pair. A distinctive feature of the proposed design is control by using a program that installed on t he user's smartphone, which also carries out the primary data processing. Data transmission is carried out over the radio channel using a Bluetooth module. Disposable cuvettes are used for measurements. This approach makes it possible to significantly redu ce both the device production costs and operating costs by eliminating most of the operations for the device preparing for working (the vast majority of existing types of viscometers require thorough flushing of all units in contact with the test medium). In addition, the proposed approach excludes the occurrence of measurement errors associated with insufficiently thorough preparation of the device for operation.

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Development of viscometric methods for studying the interaction of porphyrins with DNA

Cited by 4 publications

References 44 publications

Comprehensive Assessment of Biomolecular Interactions of Morpholine‐Based Mixed Ligand Cu(II) and Zn(II) Complexes of 2,2′‐Bipyridine as Potential Anticancer and SARS‐CoV‐2 Agents: A Synergistic Experimental and Structure‐Based Virtual Screening

Comprehensive Assessment of Biomolecular Interactions of Morpholine‐Based Mixed Ligand Cu(II) and Zn(II) Complexes of 2,2′‐Bipyridine as Potential Anticancer and SARS‐CoV‐2 Agents: A Synergistic Experimental and Structure‐Based Virtual Screening

Book of Abstracts. Albany 2019: The 20th Conversation

The design of viscometer with smartphone controlling

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