Spectroscopic probing of recognition of the G-quadruplex in c-kit promoter by small-molecule natural products

The c-kit oncogene plays important roles in cell growth and proliferation which is associated with many human tumors. In this study, electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy were used to evaluate the formation and recognition of the G-quadruplex by d(AGGGAGGGCGCTGGGAGGAGGG) in the promoter region of the c-kit oncogene. Among the twelve small natural molecules studied, three crescent-shaped small molecules (chelerythrine, jatrorrhizine and berberine, named as P1–P3) and one flexible cyclic small molecule (fangchinoline, named as P4) were found to bind to the G-quadruplex with high affinities. The melting experiments demonstrate that P1–P4 can significantly enhance the stability of the G-quadruplex with the ordering of P1 ≈ P4 > P3 > P2. Further insight into the binding mode of small molecules with the G-quadruplex by Autodock3 analysis reveals that P1–P3 prefer the end-stacking mode with the G-quadruplex through π–π interaction and P4 prefers to insert into the groove outside the G-tetrads. Thus, our research finds that four ligands (P1–P4) from small natural molecules have high affinity to, and can significantly enhance the stability of the G-quadruplex in the promoter region of the c-kit oncogene.