Interaction of bisbenzimidazole-substituted carbazole derivatives with G-quadruplexes and living cells

Abstract

G-quadruplex (G4) ligands have potential as chemotherapeutic agents because of the important roles of G4s in regulation of genomic function. Previously, we have developed a fluorescent probe (termed as BPBC) with excellent selectivity to parallel G4s, which possesses a V-shaped bisbenzimidazole-substituted carbazole planar core and two methylpiperazine side arms. Here, we further investigated the interactions of BPBC derivatives with different DNA and living cells. The spectral analysis showed that non-substituted bisbenzimidazole-substituted carbazole (7c) and bisdimethylamino-substituted 7c (7b) exhibited good selectivity to parallel G4s. The binding affinities of BPBC derivatives to parallel G4s were BPBC > 7b ≧ 7c. BPBC and 7b entered living cells and mainly located in the cytoplasma and nucleoli; 7c mainly located in the lysosome. BPBC exhibited the highest cytotoxicity with IC₅₀ around 1 μM. Our results suggest that the bisbenzimidazole-substituted carbazole core is the key factor for selectively binding BPBC derivatives to parallel G4s; the side arms can change their affinity to specific G4s, as well as their interaction with cells. Further optimization of the side arms will provide the opportunity to obtain chemotherapeutic agents targeting specific G4s in cells.