Structure of the Major G‑Quadruplex in the Human EGFR Oncogene Promoter Adopts a Unique Folding Topology with a Distinctive Snap-Back Loop

• Published in: Journal of the American Chemical Society Vol. 145; no. 29; pp. 16228 - 16237
• Main Authors: Liu, Yushuang, Li, Jinzhu, Zhang, Yongqiang, Wang, Yingying, Chen, Juannan, Bian, Yuting, Xia, Yuanzheng, Yang, Ming-Hua, Zheng, Kewei, Wang, Kai-Bo, Kong, Ling-Yi
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 26.07.2023
• Subjects: cancer therapy; colorectal neoplasms; DNA; DNA-directed DNA polymerase; glioblastoma; hepatoma; humans; hydrogen; oncogenes; promoter regions; topology; tyrosine
• DOI: 10.1021/jacs.3c05214
• ISSN: 0002-7863; 1520-5126

EGFR tyrosine kinase inhibitors have made remarkable success in targeted cancer therapy. However, therapeutic resistance inevitably occurred and EGFR-targeting therapy has been demonstrated to have limited efficacy or utility in glioblastoma, colorectal cancer, and hepatocellular carcinoma. Therefore, there is a high demand for the development of new targets to inhibit EGFR signaling. Herein, we found that the EGFR oncogene proximal promoter sequence forms a unique type of snap-back loop containing G-quadruplex (G4), which can be targeted by small molecules. For the first time, we determined the NMR solution structure of this snap-back EGFR-G4, a three-tetrad-core, parallel-stranded G4 with naturally occurring flanking residues at both the 5′-end and 3′-end. The snap-back loop located at the 3′-end region forms a stable capping structure through two stacked G-triads connected by multiple potential hydrogen bonds. Notably, the flanking residues are consistently absent in reported snap-back G4s, raising the question of whether such structures truly exist under in vivo conditions. The resolved EGFR-G4 structure has eliminated the doubt and showed distinct structural features that distinguish it from the previously reported snap-back G4s, which lack the flanking residues. Furthermore, we found that the snap-back EGFR-G4 structure is highly stable and can form on an elongated DNA template to inhibit DNA polymerase. The unprecedented high-resolution EGFR-G4 structure has thus contributed a promising molecular target for developing alternative EGFR signaling inhibitors in cancer therapeutics. Meanwhile, the two stacked triads may provide an attractive site for specific small-molecule targeting.