Structural insight into the bulge-containing KRAS oncogene promoter G-quadruplex bound to berberine and coptisine

Area of Science:

• Molecular biology
• Structural biology
• Medicinal chemistry

Background:

• KRAS is a frequently mutated oncoprotein overexpressed in many cancers, correlating with poor patient survival.
• The KRAS oncogene promoter forms a G-quadruplex structure (KRAS-G4), a potential target for small molecule drugs.
• Lack of structural data for KRAS-G4-ligand complexes impedes rational drug design.

Purpose of the Study:

• To determine the NMR solution structures of KRAS-G4 in complex with berberine and coptisine.
• To elucidate the molecular interactions between KRAS-G4 and these small molecules.
• To provide a structural basis for developing KRAS-G4-targeting anticancer drugs.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy to determine solution structures.
• Analysis of ligand-G-quadruplex complex stoichiometry and binding modes.
• Assessment of berberine and coptisine effects on KRAS mRNA levels in cancer cells.

Main Results:

• The study determined the NMR solution structures of bulge-containing KRAS-G4 bound to berberine and coptisine.
• A 2:1 binding stoichiometry was observed, with ligands forming a "quasi-triad plane" via interactions with adenine residues.
• Berberine and coptisine significantly reduced KRAS mRNA levels in cancer cells, demonstrating their biological activity.

Conclusions:

• The determined complex structures provide unprecedented molecular details of ligand interactions with KRAS-G4.
• These findings are crucial for the structure-based rational design of novel KRAS-G4-interactive anticancer drugs.
• The study offers a foundation for developing targeted therapies against KRAS-driven cancers.