Single Crystal X-Ray Structure for the Disordered Two Independent Molecules of Novel Isoflavone: Synthesis, Hirshfeld Surface Analysis, Inhibition and Docking Studies on IKKβ of 3-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-6,7-dimethoxy-4H-chromen-4-one

Abstract

The structure of the isoflavone compound, 3-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-6,7-dimethoxy-4H-chromen-4-one (5), was elucidated by 2D-NMR spectra, mass spectrum and single crystal X-ray crystallography. Compound 5, C19H16O6, was crystallized in the monoclinic space group P21/c with the cell parameters; a = 12.0654(5) Å, b =11.0666(5) Å, c = 23.9550(11) Å, β = 101.3757(16)°, V = 3135.7(2) Å3, and Z = 8. The asymmetric unit of compound 5 consists of two independent molecules 5I and 5II. Both molecules exhibit the disorder of each methylene group present in their 1,4-dioxane rings with relative occupancies of 0.599(10) (5I) and 0.812(9) (5II) for the major component A, and 0.401(10) (5I) and 0.188(9) (5II) for the minor component B, respectively. Each independent molecule revealed remarkable discrepancies in bond lengths, bond angles and dihedral angles in the disordered regions of 1,4-dioxane rings. The common feature of the molecules 5I and 5II are a chromone ring and a benzodioxin ring, which are more tilted towards each other in 5I than in 5II. An additional difference between the molecules is seen in the relative disposition of two methoxy substituents. In the crystal, the molecule 5II forms inversion dimers which are linked into chains along an a-axis direction by intermolecular C–H⋯O interactions. Additional C–H⋯O hydrogen bonds connected the molecules 5I and 5II each other to form a three-dimensional network. Hirshfeld surface analysis evaluated the relative intermolecular interactions which contribute to each crystal structure 5I and 5II. Western blot analysis demonstrated that compound 5 inhibited the TNFα-induced phosphorylation of IKKα/β, resulting in attenuating further downstream NF-κB signaling. A molecular docking study predicted the possible binding of compound 5 to the active site of IKKβ. Compound 5 showed an inhibitory effect on the clonogenicity of HCT116 human colon cancer cells. These results suggest that compound 5 can be used as a platform for the development of an anti-cancer agent targeting IKKα/β.