Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach

• Isolation of novel isoflavone, 5,6,7-trimethoxy-3-(3′,4′,5′-trimethoxyphenyl)-4H-chromen-4-one (1) from Cassia siamea leaves.
• Single-crystal X-ray analysis and DFT calculations of compound 1.
• Compounds 1 and 2 interact with CT-DNA via non-intercalative binding mode with moderate proficiencies.
• Compound 1 probably interacts with DNA through electrostatic interactions.
• Groove binding was the major interaction mode in case of compound 2.

A novel isoflavone, 5,6,7-trimethoxy-3-(3′,4′,5′-trimethoxyphenyl)-4H-chromen-4-one (1) along with a known pyranocoumarin, Seselin (2) have been isolated from the ethanolic extract of the leaves of Cassia siamea (Family: Fabaceae). Compound 1 has been reported for the first time from any natural source and has not been synthesized so far. Their structures were elucidated on the basis of chemical and physical evidences viz. elemental analysis, UV, FT-IR, 1H-NMR, 13C-NMR and mass spectral analysis. Structure of compound (1) was further authenticated by single-crystal X-ray analysis and density functional theory (DFT) calculations. A multi-technique approach employing UV–Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay, circular dichroism and viscosity studies have been utilized to probe the extent of interaction and possible binding modes of isolated compounds (1–2) with calf thymus DNA (CT-DNA). Both the compounds were found to interact with DNA via non-intercalative binding mode with moderate proficiencies. Groove binding was the major interaction mode in the case of compound 2 while compound 1 probably interacts with DNA through electrostatic interactions. These studies provide deeper insight in understanding of DNA–drug (natural products) interaction which could be helpful to improve their bioavailability for therapeutic purposes.

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