G-quadruplex-binding benzo[a]phenoxazines down-regulate c-KIT expression in human gastric carcinoma cells

Area of Science:

• Molecular Biology
• Medicinal Chemistry
• Genetics

Background:

• G-quadruplex (G4) structures are nucleic acid secondary structures of significant interest due to their roles in cellular functions and therapeutic potential.
• G4 motifs are frequently found in gene promoter regions, suggesting a link between G4 formation and gene transcriptional regulation.

Purpose of the Study:

• To identify novel G-quadruplex ligands capable of modulating gene transcription.
• To investigate the potential of these ligands as therapeutic agents, specifically targeting the c-KIT oncogene.

Main Methods:

• Utilized a functional cell-based assay to screen for G-quadruplex ligands.
• Employed a luciferase reporter system driven by the G-quadruplex-containing c-KIT promoter.
• Validated the effect of identified ligands on endogenous c-KIT expression in a human gastric carcinoma cell line.
• Performed biophysical analysis using surface plasmon resonance (SPR) to assess ligand binding affinity and selectivity.

Main Results:

• Identified two novel G-quadruplex ligands that significantly reduce transcription from the c-KIT promoter.
• Demonstrated that these ligands decrease endogenous c-KIT expression in gastric cancer cells.
• Confirmed high-affinity and preferential binding of the ligands to specific G-quadruplex structures within the c-KIT promoter compared to double-stranded DNA.

Conclusions:

• Cell-based reporter assays are effective for discovering G-quadruplex binding molecules that regulate transcription.
• Benzo[a]phenoxazine derivatives represent a promising class of compounds for targeting G-quadruplex structures.
• These findings identify novel G-quadruplex ligands with potential as antitumor agents, particularly for cancers involving c-KIT.