Aza-Macrocyclic Triphenylamine Ligands for G-Quadruplex Recognition

Deciphering the Interplay Between G-Quadruplexes and Natural/Synthetic Polyamines

The interplay between polyamines and G-quadruplexes has been largely overlooked in the literature, even though polyamines are ubiquitous metabolites in living cells and G-quadruplexes are transient regulatory elements, being both of them key regulators of biological processes. Herein, we compile the investigations connecting G-quadruplexes and biogenic polyamines to understand the biological interplay between them. Moreover, we overview the main works focused on synthetic ligands containing polyamines designed to target G-quadruplexes, aiming to unravel the structural motifs for designing potent and selective G4 ligands.

Highly Selective Fluorescent Sensors: Polyethylenimine Derivatives of Triphenylamine and Coumarin for GTP and ATP Interaction via Fluorescence Lifetime Imaging Microscopy

Chemical derivatives of polyethylenimine (PEI) receptors with either triphenylamine (TPA) or 7-hydroxy-4-methyl-coumarin (Cou) form stable complexes with adenine and guanine nucleotides in water. The host-guest complex modulation is found to be based on noncovalent molecular interactions such as π-π stacking and hydrogen bonding, which are dependent on the aromatic moieties attached to the polyaminic (PEI) backbone. PEI-TPA acts as a chemosensor with a recognition driving force based on aggregation-induced emission (AIE), involving π-π interaction between the nucleic base and TPA. It detects GTP by a chelation enhancement quenching effect of fluorescence (CHEQ) with a measured logarithm stability constant, log β = 7.7. By varying the chemical characteristics of the fluorophore, as in the PEI-Cou system, the driving force for recognition changes from a π-π interaction to an electrostatic interaction. The coumarin derivative detects ATP with a log β value one order of magnitude higher than that for GTP, allowing for the selective recognition of the two nucleotides in a 100% aqueous solution. Furthermore, fluorescence lifetime imaging microscopy (FLIM) allows for a correlation between the selectivity of PEI-TPA toward nucleotides and the morphology of the structures formed upon ATP and GTP recognition. This study offers valuable insights into the design of receptors for the selective recognition of nucleotides in water.

Design and Synthesis of Xanthone Analogues Conjugated with Aza-aromatic Substituents as Promising G-Quadruplex Stabilizing Ligands and their Selective Cancer Cell Cytotoxic Action

We have examined the stabilization of higher-order noncanonical G-quadruplex (G4) DNA structures formed by the G-rich sequences in the promoter region of oncogenes such as c-MYC, c-KIT, VEGF and BCl2 by newly synthesized, novel nitrogen-containing aromatics conjugated to xanthone moiety. Compounds with N-heterocyclic substituents such as pyridine (XNiso), benzimidazole (XBIm), quinoxaline (XQX) and fluorophore dansyl (XDan) showed greater effectiveness in stabilizing the G4 DNA as well as selective cytotoxicity for cancer cells (mainly A549) over normal cells both in terms of UV-Vis spectral titrations and cytotoxicity assay. Both fluorescence spectral titrimetric measurements and circular dichroism (CD) melting experiments further substantiated the G4 stabilization phenomenon by these small-molecular ligands. In addition, these compounds could induce the formation of parallel G4 structures in the absence of any added salt condition in Tris⋅HCl buffer at 25 °C. In a polymerase stop assay, the formation of stable G4 structures in the promoter of oncogenes and halting of DNA synthesis in the presence of the above-mentioned compounds was demonstrated by using oncogene promoter as the DNA synthesis template. Apoptosis-mediated cell death of the cancer cells was proved by Annexin V-PI dual staining assay and cell-cycle arrest occurred in the S phase of the cell cycles. The plausible mode of binding involves the stacking of the xanthone core on the G4 DNA plane with the possibility of interaction with the 5'-overhang as indicated by molecular dynamics simulation studies.

Development of potent tripodal G-quadruplex DNA binders and their efficient delivery to cancer cells by aptamer functionalised liposomes

Two new ligands (TPB3P and TPB3Py) showing a strong stabilisation effect and good selectivity for G4 over duplex DNAs have been synthesised. The ligands hold three analogous polyamine pendant arms (TPA3P and TPA3Py) but differ in the central aromatic core, which is a triphenylbenzene moiety instead of a triphenylamine moiety. Both TPB3P and TPB3Py exhibit high cytotoxicity in MCF-7, LN229 and HeLa cancer cells in contrast to TPA-based ligands, which exhibit no significant cytotoxicity. Moreover, the most potent G4 binders have been encapsulated in liposomes and AS1411 aptamer-targeted liposomes reaching nanomolar IC₅₀ values for the most cytotoxic systems.

Modulating the G-Quadruplex and Duplex DNA Binding by Controlling the Charge of Fluorescent Molecules

Two fluorescent and non-toxic spirobifluorene molecules bearing either positive (Spiro-NMe3) or negative (Spiro-SO3) charged moieties attached to the same aromatic structure have been investigated as binders for DNA. The novel Spiro-NMe3 containing four alkylammonium substituents interacts with G-quadruplex (G4) DNA structures and shows preference for G4s over duplex by means of FRET melting and fluorescence experiments. The interaction is governed by the charged substituents of the ligands as deduced from the lower binding of the sulfonate analogue (Spiro-SO3). On the contrary, Spiro-SO3 exhibits higher binding affinity to duplex DNA structure than to G4. Both molecules show a moderate quenching of the fluorescence upon DNA binding. The confocal microscopy evaluation shows the internalization of both molecules in HeLa cells and their lysosomal accumulation.

Cucurbituril hosts as promoters of aggregation induced emission of triphenylamine derivatives

Three ligands bearing triphenylamine as a core and one, two or three acyclic polyamine chains, TPA1p, TPA2p and TPA3p, respectively, have been studied by potentiometric and photophysical (UV-Vis, steady-state and time-resolved fluorescence) techniques. The host-guest interaction with cucurbit[7]uril, CB7, has been investigated in aqueous solution showing aggregation induced emission behaviour when encapsulated into a CB7 cavity. From fluorescence emission it is revealed that the charged polyamine chains are the unit entering into CB7 and from the Job plots the stoichiometries are found to vary from 1 : 1 to 1 : 3 L : CB7 ratios. Interactions of the charged amines with the portals of CB7 restrict rotation of the benzene units in the triphenylamine backbone (free rotor effect), decreasing the radiationless internal conversion channel at the expense of the enhancement of fluorescence. Dynamic light scattering and resonance Rayleigh scattering experiments show that TPA3p-CB7 complexes involve formation of aggregates with a mean size of 126 ± 5 nm and a dispersity factor of 0.117, indicating a monodisperse distribution and supporting the important conclusions of this work: formation of emissive aggregates through the AIE effect.

Recent progresses in the chemistry of 12-membered pyridine-containing tetraazamacrocycles: From synthesis to catalysis

This article provides an overview (non-comprehensive) on recent developments regarding pyridine-containing 12-membered tetraazamacrocycles with pyclen or Py2N2 backbones and their metal complexes from 2017 to the present. Firstly, the synthesis...

Cluster dirhenium(III) cis-dicarboxylates with α-amino acids ligands as mighty selective G4s binders

The synthesis of four dirhenium(III) cis-dicarboxylates with the α-amino acids residues Asp (I), Glu (II), Phe (III) and Tyr (IV) is presented. The G-quadruplex stabilization potential was evaluated by fluorescence resonance energy transfer - melting analysis. All derivatives show specific binding to c-kit1 quadruplex, while II and IV have also strong stabilization activity to HTelo21 quadruplex. At the same time, the compounds do not show any stabilization activity for ds26 DNA, which suggests unique mechanisms of molecular DNA recognition for these complexes.

Macrocyclic Pyclen-Based Gd3+ Complex with High Relaxivity and pH Response

We report the synthesis and characterization of the macrocyclic ligand 2,2'-((2-(3,9-bis(carboxymethyl)-3,6,9-triaza-1(2,6)-pyridinacyclodecaphane-6-yl)ethyl)azanediyl)diacetic acid (H₄L) and several of its complexes with lanthanide ions. The structure of the free ligand was determined using X-ray diffraction measurements. Two N atoms of the pyclen moiety in the trans position are protonated in the solid state, together with the exocyclic N atom and one of the carboxylate groups of the ligand. The relaxivity of the Gd³⁺ complex was found to increase from 6.7 mM^-1 s^-1 at pH 8.6 to 8.5 mM^-1 s^-1 below pH ≈ 6.0. Luminescence lifetime measurements recorded from H₂O and D₂O solutions of the Eu³⁺ complex evidence the presence of a single complex species in solution at low pH (∼5.0) that contains two inner-sphere water molecules. DFT calculations suggest that the coordination environment of the Ln³⁺ ion is fulfilled by the four N atoms of the pyclen unit, two oxygen atoms of the macrocyclic acetate groups, and an oxygen atom of an exocyclic carboxylate group. The two inner-sphere water molecules complete coordination number nine around the metal ion. At high pH (∼9.3), the lifetime of the excited ⁵D₀ level of Eu³⁺ displays a biexponential behavior that can be attributed to the presence of two species in solution with hydration numbers of q = 0 and q = 1. The ¹H NMR and DOSY spectra recorded from solutions of the Eu³⁺ and Y³⁺ complexes reveal a structural change triggered by pH and the formation of small aggregates at high pH values.

Development of Polyamine-Substituted Triphenylamine Ligands with High Affinity and Selectivity for G-Quadruplex DNA

Currently, significant efforts are devoted to designing small molecules able to bind selectively to guanine quadruplexes (G4s). These noncanonical DNA structures are implicated in various important biological processes and have been identified as potential targets for drug development. Previously, a series of triphenylamine (TPA)-based compounds, including macrocyclic polyamines, that displayed high affinity towards G4 DNA were reported. Following this initial work, herein a series of second-generation compounds, in which the central TPA has been functionalised with flexible and adaptive linear polyamines, are presented with the aim of maximising the selectivity towards G4 DNA. The acid-base properties of the new derivatives have been studied by means of potentiometric titrations, UV/Vis and fluorescence emission spectroscopy. The interaction with G4s and duplex DNA has been explored by using FRET melting assays, fluorescence spectroscopy and circular dichroism. Compared with previous TPA derivatives with macrocyclic substituents, the new ligands reported herein retain the G4 affinity, but display two orders of magnitude higher selectivity for G4 versus duplex DNA; this is most likely due to the ability of the linear substituents to embrace the G4 structure.

Diphenylaminostyryl-substituted quinolizinium derivatives as fluorescent light-up probes for duplex and quadruplex DNA

(E)-2-[1'-((Diphenylamino)styryl)quinolizinium (3a) and 2,2'-{(phenylimino)-bis[(E)-1'',1'''-styryl]}-bis[quinolizinium] (3b) were synthesized, and their interactions with duplex DNA and quadruplex DNA were investigated with a particular focus on their ability to operate as DNA-sensitive fluorescent probes. Due to the significantly different size and steric demand of these quinolizinium derivatives they exhibit different binding modes. Thus, 3a intercalates into duplex DNA and binds through π stacking to quadruplex DNA, whereas 3b favours groove binding to both DNA forms. The emission intensity of these compounds is very low in aqueous solution, but it increases drastically upon association with duplex DNA by a factor of 11 (3a) and >100 (3b) and with quadruplex DNA by a factor of >100 (3a) and 10 (3b), with emission bands between 600 and 750 nm.