De Novo Design of Selective Quadruplex–Duplex Junction Ligands and Structural Characterisation of Their Binding Mode: Targeting the G4 Hot‐Spot

Abstract

Targeting the interface between DNA quadruplex and duplex regions by small molecules holds significant promise in both therapeutics and nanotechnology. Herein, a new pharmacophore is reported, which selectively binds with high affinity to quadruplex–duplex junctions, while presenting a poorer affinity for G‐quadruplex or duplex DNA alone. Ligands complying with the reported pharmacophore exhibit a significant affinity and selectivity for quadruplex–duplex junctions, including the one observed in the HIV‐1 LTR‐III sequence. The structure of the complex between a quadruplex–duplex junction with a ligand of this family has been determined by NMR methods. According to these data, the remarkable selectivity of this structural motif for quadruplex–duplex junctions is achieved through an unprecedented interaction mode so far unexploited in medicinal and biological chemistry: the insertion of a benzylic ammonium moiety into the centre of the partially exposed G‐tetrad at the interface with the duplex. Further decoration of the described scaffolds with additional fragments opens up the road to the development of selective ligands for G‐quadruplex‐forming regions of the genome.

Structure of i-Motif/Duplex Junctions at Neutral pH

“…Since DNA is mainly a double helix in the cell, local G-quadruplex or i-motif formation entails the occurrence of interfaces (junctions) with canonical B-form DNA regions. In recent years, G-quadruplex/duplex junctions have been extensively studied and found to be an interesting target for selective recognition . However, very little is known about the structure of i-motif/duplex junctions (IDJs), although they are probably as common as those involving G-quadruplexes …”

Probing GFP Chromophore Analogs as Anti-HIV Agents Targeting LTR-III G-Quadruplex

“…The titration data were successfully approximated by simple chemical reaction A + B = AB, that implies one to one stoichiometry of binding that is consistent with literature data (Suppl. S8) [17]. The dissociation constant for the LTR-III/ZS260.1 complex (Kd) was on the order of 3 μM.…”

“…There are three major structural types of G4-interacting compounds: (1) fused aromatic polycyclic systems; (2) non-fused aromatic systems, in which the aromatic fragments are connected by short linkers; and (3) macrocyclic compounds (Figure 1B) [1]. Recently, benzylamine-like motifs have been successively used to selectively bind with high affinity to quadruplexduplex junctions of LTR-III G4, and they could be attributed to the class of the fused aromatic polycyclic systems [17].…”

Expanding the Topological Landscape by a G‐Column Flip of a Parallel G‐Quadruplex

“…Refolding of the parallel L11AT quadruplex into a hybrid‐type quadruplex upon Br G substitutions in its fourth G‐tract results in a coaxial stacking of the stem‐loop duplex onto the outer G‐tetrad with the formation of a quadruplex‐duplex interface. Quadruplex‐duplex (Q−D) junctions may serve as specific recognition elements for ligands [14,15] . In fact, a corresponding Q−D junction has recently been shown to constitute a favorable binding site for a ligand termed PIQ which is based on a phenyl‐substituted indoloquinoline heterocyclic ring system [16] .…”

“…Quadruplex‐duplex (Q−D) junctions may serve as specific recognition elements for ligands. [ 14 , 15 ] In fact, a corresponding Q−D junction has recently been shown to constitute a favorable binding site for a ligand termed PIQ which is based on a phenyl‐substituted indoloquinoline heterocyclic ring system. [16] Isothermal titration calorimetry (ITC) was initially employed to probe PIQ binding to the novel hybrid‐2R G ‐ quadruplex with its stacked hairpin lateral loop.…”