Rational design of small-molecules to recognize G-quadruplexes of c-MYC promoter and telomere and the evaluation of their in vivo antitumor activity against breast cancer

Abstract

DNA G4-structures from human c-MYC promoter and telomere are considered as important drug targets; however, the developing of small-molecule-based fluorescent binding ligands that are highly selective in targeting these G4-structures over other types of nucleic acids is challenging. We herein report a new approach of designing small molecules based on a non-selective thiazole orange scaffold to provide two-directional and multi-site interactions with flanking residues and loops of the G4-motif for better selectivity. The ligands are designed to establish multi-site interactions in the G4-binding pocket. This structural feature may render the molecules higher selectivity toward c-MYC G4s than other structures. The ligand–G4 interaction studied with 1H NMR may suggest a stacking interaction with the terminal G-tetrad. Moreover, the intracellular co-localization study with BG4 and cellular competition experiments with BRACO-19 may suggest that the binding targets of the ligands in cells are most probably G4-structures. Furthermore, the ligands that either preferentially bind to c-MYC promoter or telomeric G4s are able to downregulate markedly the c-MYC and hTERT gene expression in MCF-7 cells, and induce senescence and DNA damage to cancer cells. The in vivo antitumor activity of the ligands in MCF-7 tumor-bearing mice is also demonstrated.

Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules

“…As for 4c, the result is discussed based on the usual end-stacking favoured by the presence/absence of hindering by the loops, with the addition of some interesting analysis on fluorescence lifetimes and by the careful check of the absence of positive induced dichroic signals (ICD), taken as an indicator of groove binding to G4 [58]. On the other hand, Figure 4d reports the phenylaminoacridine also known as BRACO19, which constitutes a golden reference for G4 binders, to such an extent that it can be used as a fluorescent tag for exchange experiments to prove G4 binding by the competitor [60]. The paper above cited on BRACO19/G4 interaction [59] uses molecular dynamics including explicit solvents to improve a previous theoretical work [61]: both papers emphasise the higher affinity for a G-quartet stacked binding mode.…”

RNA Modification in Inflammatory Bowel Diseases

“…Recent studies have indicated the activity of DNA G4 structures as small molecules against breast cancer by targeting the promoter of the human oncogene c-MYC and telomeres [ 47 ]. These small molecules are based on a non-selective thiazole orange scaffold to provide multifaceted interactions with flanking residues [ 47 ].…”

“…Recent studies have indicated the activity of DNA G4 structures as small molecules against breast cancer by targeting the promoter of the human oncogene c-MYC and telomeres [ 47 ]. These small molecules are based on a non-selective thiazole orange scaffold to provide multifaceted interactions with flanking residues [ 47 ]. For example, the transcription of the KRAS oncogene is controlled by a G-rich motif, which is located immediately upstream of the transcriptional start site.…”

Putative G-quadruplex Formation in the Upstream Region of mTOR Gene

“…G-quadruplexes (G4) are widely present throughout the human genome especially in the promoters 36,37 , telomeres 38,39,40 , UTRs 41,42 , intronic regions of genes involved in development, survival and proliferation 43,44 . These four-stranded nucleic acid structures are also increasingly being recognized as regulatory elements for replication, transcription, and other important regulatory roles 45,46,47,48 .…”