Structure–activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two analogues probed with comparative transcriptome profiling and molecular modeling

Abstract

The tetrasubstituted naphthalene diimide compound QN-302 binds to G-quadruplex (G4) DNA structures. It shows high potency in pancreatic ductal adenocarcinoma (PDAC) cells and inhibits the transcription of cancer-related genes in these cells and in PDAC animal models. It is currently in Phase 1a clinical evaluation as an anticancer drug. A study of structure–activity relationships of QN-302 and two related analogues (CM03 and SOP1247) is reported here. These have been probed using comparisons of transcriptional profiles from whole-genome RNA-seq analyses, together with molecular modelling and molecular dynamics simulations. Compounds CM03 and SOP1247 differ by the presence of a methoxy substituent in the latter: these two compounds have closely similar transcriptional profiles. Whereas QN-302 (with an additional benzyl-pyrrolidine group), although also showing down-regulatory effects in the same cancer-related pathways, has effects on distinct genes, for example in the hedgehog pathway. This distinctive pattern of genes affected by QN-302 is hypothesized to contribute to its superior potency compared to CM03 and SOP1247. Its enhanced ability to stabilize G4 structures has been attributed to its benzyl-pyrrolidine substituent fitting into and filling most of the space in a G4 groove compared to the hydrogen atom in CM03 or the methoxy group substituent in SOP1247.

Structural Motifs at the Telomeres and Their Role in Regulatory Pathways

“…114 It is worth mentioning that a G4 targeting clinical candidate� QN302�has been approved for Phase 1 clinical trials by the FDA for pancreatic ductal adenocarcinoma. 118,119 Crucial to the discussion of G4 is the presence of Gquadruplex binding proteins (G4BPs) other than POT1 that perform several important functions like providing stability to the G4 complex as well as facilitating its unfolding. 120 The basic categories of G4BPs are based on the regulatory mechanisms and functional interactions these proteins have with G4s.…”

“…The G4s are thermodynamically stable with melt temperature above dsDNA and can be further stabilized by the presence of small molecule ligands . It is worth mentioning that a G4 targeting clinical candidateQN302has been approved for Phase 1 clinical trials by the FDA for pancreatic ductal adenocarcinoma. , …”

“… 114 It is worth mentioning that a G4 targeting clinical candidate—QN302—has been approved for Phase 1 clinical trials by the FDA for pancreatic ductal adenocarcinoma. 118 , 119 …”

The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery

“…123 The development of an effective and flexible synthetic protocol has further allowed for easy chemical modification toward druglikeness, 124 such as that underlined by the phase I clinical trial running with QN-302 (Figure 4, ClinicalTrials.gov ID NCT06086522). 125 Two putative G4-forming sequences have been identified in the E. coli genome (strain LMG8223) using the G4-iM Grinder bioinformatics tool 126 by Cebrian et al 124 The propensity of these sequences (i.e., EC-6 and EC-9, Table 1) to form G4s was confirmed by CD spectra recorded in the presence of 100 mM K + , which showed a predominant parallel topology with a maximum peak at ∼264 nm and a minimum peak at ∼240 nm. The stabilizing effect of the most promising hit NDI-10 (Figure 5) was confirmed by FRET melting and CD melting assays, showing a remarkable stabilization of the tested sequences by the small molecule.…”

“…coli has been recently used as a model system in the evaluation of the G4 stabilizing activity by a series of naphthalene diimides (NDIs), a profitable family of electron-deficient and flat molecules that have been thoroughly exploited in several fields including supramolecular and material chemistry, especially within the last two decades. − Among the various applications of NDIs, of particular interest for this Review is their capability to stack on the top of electron-rich G-quartets in DNA G4s . The development of an effective and flexible synthetic protocol has further allowed for easy chemical modification toward drug-likeness, such as that underlined by the phase I clinical trial running with QN-302 (Figure , ClinicalTrials.gov ID NCT06086522) …”