Synthesis, G‐Quadruplex Stabilisation, Docking Studies, and Effect on Cancer Cells of Indolo[3,2‐b]quinolines with One, Two, or Three Basic Side Chains

Abstract

G‐quadruplex (G4) DNA structures in telomeres and oncogenic promoter regions are potential targets for cancer therapy, and G4 ligands have been shown to modulate telomerase activity and oncogene transcription. Herein we report the synthesis and G4 thermal stabilisation effects, determined by FRET melting assays, of 20 indolo[3,2‐b]quinolines mono‐, di‐, and trisubstituted with basic side chains. Molecular modelling studies were also performed in an attempt to rationalise the ligands′ binding poses with G4. Overall, the results suggest that ligand binding and G4 DNA thermal stabilisation increase with an N5‐methyl or a 7‐carboxylate group and propylamine side chains, whereas selectivity between G4 and duplex DNA appears to be modulated by the number and relative position of basic side chains. From all the indoloquinoline derivatives studied, the novel trisubstituted compounds 3 d and 4 d, bearing a 7‐(aminoalkyl)carboxylate side chain, stand out as the most promising compounds; they show high G4 thermal stabilisation (ΔTm values between 17 and 8 °C) with an inter‐G4 ΔTm trend of Hsp90A>KRas21R≈F21T>c‐Kit2, 10‐fold selectivity for G4 over duplex DNA, and 100‐fold selectivity for the HCT116 cancer cell line (IC50 and IC90: <10 μM) over primary rat hepatocytes. Compounds 3 d and 4 d also decreased protein expression levels of Hsp90 and KRas in HCT116 cancer cells.

KRAS oncogene repression in colon cancer cell lines by G-quadruplex binding indolo[3,2-c]quinolines

“…Structure-activity relationships established on the basis of increased T m determined by FRET were in agreement with those previously reported for IQb series of compounds22. Based on these results compounds 2d (with one alkyldiamine side chain) and 3e (with two alkyldiamine side chains) were selected for further in vitro studies.…”

“…Competition binding studies have previously shown that some small molecules can bind preferentially to quadruplex compared to triplex or duplex structures3132, and/or have differing inductive stabilization effects over G4 DNA sequences of different lengths. This is the case for those IQb compounds with 3 basic side chains in positions 7, 10 and 11, which showed higher Δ T m values for 21 mer G4-forming DNA sequences (KRAS21R, HT21, HSP90A) compared to 27 mer G4 DNA (cKit1) or longer G4 DNA structures with more complex topologies (HIF-1α)22. We report here that a small molecule can preferentially stabilize one G4 forming sequence over another with the same number of nucleotides.…”

“…The ability of indolo[3,2- c ]quinolines to stabilize DNA sequences was investigated using a Fluorescence Resonance Energy Transfer (FRET) assay as reported elsewhere22.…”

“…In the past decade an intensive search for small-molecules as potent G4 ligands has led to the identification of a large number with anti-proliferative activity in cells1718. However, to the best of our knowledge, only three small-molecule chemical types have been identified as KRAS / HRAS expression down-regulators: low-membrane permeable porphyrins12131920, of which TMPyP4 is the most studied; guanidino anthratiophenediones21 and indolo[3,2- b ]quinolines (IQb)22. The in vitro structure-activity studies performed with a small library of IQb compounds has suggested that selectivity for G4 and inter-G4 could be modulated by the number and relative position of basic side chains.…”

“…The in vitro structure-activity studies performed with a small library of IQb compounds has suggested that selectivity for G4 and inter-G4 could be modulated by the number and relative position of basic side chains. Moreover, we have identified two compounds with anti-proliferative activity, selective for human colon cancer cells HCT116 compared to rat hepatocytes and a greater capacity to decrease p21 KRAS levels compared to HSP90 protein22.…”