Bisindolylmaleimide Ligands Stabilize c-MYC G-Quadruplex DNA Structure and Downregulate Gene Expression

Area of Science:

• Medicinal Chemistry
• Chemical Biology
• Genomics

Background:

• G-quadruplex (G4) structures are crucial in biological processes like gene regulation and telomere maintenance.
• Targeting G4 structures with small molecules offers therapeutic potential for diseases, including cancer.
• Developing selective G4 ligands is essential for precise therapeutic intervention.

Purpose of the Study:

• To synthesize and characterize novel bisindolylmaleimide (BIM) based ligands.
• To investigate the preferential binding and stabilization of BIM ligands towards specific G-quadruplex structures.
• To evaluate the therapeutic potential of BIM ligands, including their effect on gene expression and cytotoxicity.

Main Methods:

• Synthesis of bisindolylmaleimide (BIM) compounds.
• G-quadruplex (G4) stabilization assays, including DNA polymerase stop assays.
• Nuclear Magnetic Resonance (NMR) titration studies to determine binding affinity and mode.
• Molecular modeling and dynamics simulations.
• Cytotoxicity assays on HeLa cells and gene expression analysis.

Main Results:

• BIM ligands preferentially stabilize parallel G4 structures of c-MYC and c-KIT oncogenes over telomeric h-RAS1 G4 and duplex DNA.
• DNA polymerase stop assays confirmed selective G4 stabilization at the c-MYC sequence.
• NMR studies revealed a 2:1 complex formation between the lead ligand BIM-Pr1 and c-MYC G4 DNA with a K_D of 38 ± 5 μM.
• Molecular modeling supported the ligand's stacking interaction with G4 quartets.
• BIM ligands demonstrated cytotoxicity in HeLa cells and downregulated c-MYC gene expression.

Conclusions:

• Bisindolylmaleimide scaffolds represent a novel class of potent G-quadruplex targeting agents.
• The developed BIM ligands exhibit selectivity for oncogenic G4 structures, offering a promising therapeutic strategy.
• These findings pave the way for the development of G4-based cancer therapies.