An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations

Tanmoy Saha; Subrahmanyam Sappati; Saurabh Das

doi:10.1016/j.ijbiomac.2023.125305

An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations

Abstract

An important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule of water bound to ZnII. It arrests degradation of HCur to a considerable extent that was realized by taking it in phosphate buffer and in biological milieu. The structure was obtained by DFT calculations. Stable adduct formation was identified between optimized structures of HCur and [Zn(Cur)] with DNA (PDB ID: 1BNA) through experiments validated with multiscale modeling approach. Molecular docking studies provide 2D and 3D representations of binding of HCur and [Zn(Cur)] through different non-covalent interactions with the nucleotides of the chosen DNA. Through molecular dynamics simulation, a detailed understanding of binding pattern and key structural characteristics of the generated DNA-complex was obtained following analysis by RMSD, RMSF, radius of gyration, SASA and aspects like formation of hydrogen bonds. Experimental studies provide binding constants for [Zn(Cur)] with calf thymus DNA at 25 °C that effectively helps one to realize its high affinity towards DNA. In the absence of an experimental binding study of HCur with DNA, owing to its tendency to degrade in solution, a theoretical analysis of the binding of HCur to DNA is extremely helpful. Besides, both experimental and simulated binding of [Zn(Cur)] to DNA may be considered as a case of pseudo-binding of HCur to DNA. In a way, such studies on interaction with DNA helps one to identify HCur's affinity for cellular target DNA, not realized through experiments. The entire investigation is an understanding of experimental and theoretical approaches that has been compared continuously, being particularly useful when a molecule's interaction with a biological target cannot realized experimentally.

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Keywords

CURCUMINZNIIDFTMOLECULAR DOCKINGMOLECULAR DYNAMIC SIMULATIONRMSDRMSFRADIUS OF GYRATIONSASAHYDROGEN BONDS

Details

Category:

Articles

Type:

artykuły w czasopismach

Published in:

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES no. 245,
ISSN: 0141-8130

Language:

English

Publication year:

2023

Bibliographic description:

Saha T., Sappati S., Das S.: An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations// INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES -Vol. 245, (2023), s.125305-

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