Evidence on selective binding to G-quadruplex DNA of isoflavones from Maclura pomifera by mass spectrometry and molecular docking

G-quadruplex DNA stabilization mediated by small molecules is an attractive approach to modulate the transcription of guanine-rich sequences and contrast unregulated cell proliferation. Natural alkaloids have been reported to target this macromolecular arrangement, and such mechanism may be among these underlying the antiproliferative effect of some flavonoids. The binding affinity for G-quadruplex and double stranded DNA of 4 isoflavones from Maclura pomifera, namely osajin, pomiferin, scandenone and auriculasin, was evaluated using electrospray mass spectrometry (ESI-MS). The experiments pointed out that osajin and scandenone preferentially bind G-quadruplex. Moreover, since G-quadruplex stabilization is a crucial aim for triggering biological effects such as gene expression, collision-induced dissociation (CID) assays were performed to study the relative gas-phase kinetic stability of the DNA/ligand complexes. Osajin was identified as the best G-quadruplex stabilizer of the set, and in silico docking studies indicate that stacking is the preferred interaction motif of this natural compound.

Automated summary

This study showed that natural alkaloids from Maclura pomifera, particularly osajin and scandenone, preferentially bind to G-quadruplex DNA, with osajin identified as the best stabilizer. In silico docking studies suggested that stacking is the preferred interaction motif of osajin in stabilizing G-quadruplex.