Indoloquinoline Ligands Favor Intercalation at Quadruplex-Duplex Interfaces

Quadruplex-duplex (Q-D) junctions are increasingly considered promising targets for medicinal and technological applications. Here, a Q-D hybrid with a hairpin-type snapback loop coaxially stacked onto the quadruplex 3'-outer tetrad was designed and employed as a target structure for the indoloquinoline ligand SYUIQ-5. NMR spectral analysis demonstrated high-affinity binding of the ligand at the quadruplex-duplex interface with association constants determined by isothermal titration calorimetry of about 10(7) M-1 and large exothermicities Delta H degrees of -14 kcal/mol in a 120 mM K+ buffer at 40 degrees C. Determination of the ligand-bound hybrid structure revealed intercalation of SYUIQ-5 between 3'-outer tetrad and the neighboring CG base pair, maximizing pi-pi stacking as well as electrostatic interactions with guanine carbonyl groups in close vicinity to the positively charged protonated quinoline nitrogen of the tetracyclic indoloquinoline. Exhibiting considerable flexibility, the SYUIQ-5 sidechain resides in the duplex minor groove. Based on comparative binding studies with the non-substituted N5-methylated indoloquinoline cryptolepine, the sidechain is suggested to confer additional affinity and to fix the alignment of the intercalated indoloquinoline aromatic core. However, selectivity for the Q-D junction mostly relies on the geometry and charge distribution of the indoloquinoline ring system. The presented results are expected to provide valuable guidelines for the design of ligands specifically targeting Q-D interfaces.

Automated summary

Quadruplex-duplex (Q-D) junctions have potential for medicinal and technological applications. In this study, a Q-D hybrid with a hairpin-type snapback loop was designed as a target structure for the indoloquinoline ligand SYUIQ-5. NMR analysis showed that SYUIQ-5 binds strongly to the quadruplex-duplex interface, and the binding process is exothermic. The ligand intercalates between the quadruplex 3'-outer tetrad and the neighboring CG base pair, maximizing pi-pi stacking and electrostatic interactions. The flexible sidechain of SYUIQ-5 resides in the duplex minor groove. The results provide valuable insights for the design of ligands targeting Q-D interfaces.