Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex

Abstract

G-quadruplexes (G4s) are noncanonical DNA structures that frequently occur in the promoter regions of oncogenes, such as MYC, and regulate gene expression. Although G4s are attractive therapeutic targets, ligands capable of discriminating between different G4 structures are rare. Here, we describe DC-34, a small molecule that potently downregulates MYC transcription in cancer cells by a G4-dependent mechanism. Inhibition by DC-34 is significantly greater for MYC than other G4-driven genes. We use chemical, biophysical, biological, and structural studies to demonstrate a molecular rationale for the recognition of the MYC G4. We solve the structure of the MYC G4 in complex with DC-34 by NMR spectroscopy and illustrate specific contacts responsible for affinity and selectivity. Modification of DC-34 reveals features required for G4 affinity, biological activity, and validates the derived NMR structure. This work advances the design of quadruplex-interacting small molecules to control gene expression in therapeutic areas such as cancer.

Mission Possible: Advances in MYC Therapeutic Targeting in Cancer

“…In contrast to BRD4 inhibitors, which indirectly inhibit MYC transcription, small molecules designed to bind and stabilize the G-quadruplexes associated with individual genes provides a unique way to target potentially undruggable oncogenes [79][80][81]. Studies have shown that small molecules, such as GQC-05, Cz1, IZCZ-3, and DC-34, are capable of binding and stabilizing G-quadruplexes within the nuclease hypersensitive element (NHE) III region of the MYC promoter, resulting in the suppression of MYC messenger RNA (mRNA) and protein and an induction of cytotoxicity [82][83][84][85][86][87]. Similarly, a study by Bouvard et al [88] demonstrates that the small molecule stauprimide inhibits the transcription factor NME2 from being recruited to the NHE III region, stabilizing the MYC G-quadruplex, and selectively reducing MYC transcriptional gene programs.…”

Transcription factor recruitment by parallel G-quadruplexes to promote transcription: the case of herpes simplex virus-1 ICP4

“…Un2L2 is composed of 9 G-tracts, ranging from three to nine G bases each, gp054dL3 of ten G-tracts of 4-8 Gs each. Two additional G4-forming sequences were used: the 28 nt-long LTR-III from the HIV-1 LTR promoter (6 G-tracts of 2-3 Gs) (Butovskaya et al, 2018;Perrone et al, 2013), and the 26 nt-long myc G4-forming region from the myc oncogene promoter (6 G-tracts of 2-4 Gs) (Calabrese et al, 2018;Yang and Hurley, 2006) (Table S1). These two sequences were used as positive controls, representing well characterized viral and cellular G4s, respectively.…”

G-Quadruplex targeting ligands: A hope and a new horizon in Cancer Therapeutics

“…Ligands containing amino groups and (or) side chains can interact with the grooves, loops, and the negatively charged phosphate backbone of the G4s 50,51 . The amino groups become positively charged by protonation or methylation, which may result in better recognition and stronger binding to the grooves as well as to the negatively charged phosphate backbone through electrostatic interactions 52,53 . The side chains can recognize the loop bases and grooves by forming hydrogen bonds, which also improves the water solubility of the ligands.…”

“…Research has indicated that although planar ligands can insert into the G-tetrad layers, charged molecules are more inclined to interact with the grooves, loops or backbones of G -quadruplex structures 53,54 .…”