X-ray crystal structure of embelin and its DFT scavenging of superoxide radical

5 years ago

X-ray crystal structure of embelin and its DFT scavenging of superoxide radical

Miriam Rossi, Sarah Paumier, Francesco Caruso

Embelin is a phytochemical component of tropical plants that have a long history of being used in ethnic pharmacology in various parts of the world, including Ayurdvedic and Chinese medicinal texts. Many modern studies confirm its promise as a medicinal compound. The X-ray crystal structure determination of embelin shows a remarkably ordered alkyl chain and particularly strong pi–pi interactions for a nonaromatic system. The molecule has a torsion angle of 67° between the ring and the alkyl chain of the molecule and differs markedly from that seen when embelin is embedded in the plasminogen activator inhibitor-1 (PAI-1) binding site (almost planar—with about 10° torsion angle). This suggests that embelin's flexible structural skeleton can be useful in biological environment. Apart from this, its many biological activities likely depend on embelin's hydrophobic nonpolar tail that allows a variety of interactions. Computationally, we evaluated embelin's sequestering ability toward the superoxide radical and see that embelin executes this reaction in a novel manner. Namely, as shown by our DFT calculations, instead of releasing a H atom to the superoxide radical to form the anionic species O2H-, embelin prefers to accept an electron from the superoxide radical, which then transforms into molecular oxygen, O2. © 2017 Wiley Periodicals, Inc. A remarkably ordered alkyl chain and a particularly strong stacking intermolecular interaction for a non-aromatic system.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.24915