Structure-Informed Design of Distinct Parallel G-Quadruplex Stabilizers for KRAS-Driven Cancer Therapy

Area of Science:

• Medicinal Chemistry
• Molecular Biology
• Oncology

Background:

• Targeting G-quadruplexes (G4s) in oncogene promoters is a promising cancer therapy approach.
• Development of potent and diverse G4-targeting ligands remains a challenge.

Purpose of the Study:

• To identify novel G4 stabilizers from natural products.
• To rationally design and synthesize improved G4-targeting ligands based on structural insights.
• To evaluate the therapeutic potential of novel ligands against KRAS-driven cancers.

Main Methods:

• Screening of a natural product library to identify G4 stabilizers.
• Structural analysis of ligand-G4 interactions.
• Rational design and synthesis of G4 ligand analogues.
• In vitro antiproliferative assays and biophysical binding studies.
• NMR structural determination of G4-ligand complexes.
• Functional assays assessing oncogene transcription suppression, G4 induction, and DNA damage.
• Inhibition studies using patient-derived colorectal tumor organoids.

Main Results:

• Dehydroevodiamine (DEE) was identified as a novel stabilizer of the KRAS proximal promoter G4 (KRAS-G4).
• A synthesized analogue, 7i, exhibited 9-fold higher binding affinity and 20-fold greater antiproliferative activity than DEE.
• The KRAS-G4-7i complex revealed a unique dual-binding mode with extensive π-π stacking and hydrogen bonding.
• Compound 7i suppressed oncogene transcription, induced genome-wide G4 formation, triggered DNA damage in colorectal cancer cells, and inhibited tumor organoid growth.

Conclusions:

• A structural framework for designing parallel G4-targeting ligands was established.
• Compound 7i represents a promising lead candidate for targeting KRAS-driven cancers.
• This study highlights an alternative G4-based therapeutic strategy for human malignancies.