Interrogation of G-quadruplex–protein interactions

G-quadruplexes in cancer-related gene promoters: from identification to therapeutic targeting

INTRODUCTION

Guanine-rich DNA sequences can fold into four-stranded noncanonical secondary structures called G-quadruplexes (G4s) which are widely distributed in functional regions of the human genome, such as telomeres and gene promoter regions. Compelling evidence suggests their involvement in key genome functions such as gene expression and genome stability. Notably, the abundance of G4-forming sequences near transcription start sites suggests their potential involvement in regulating oncogenes.

AREAS COVERED

This review provides an overview of current knowledge on G4s in human oncogene promoters. The most representative G4-binding ligands have also been documented. The objective of this work is to present a comprehensive overview of the most promising targets for the development of novel and highly specific anticancer drugs capable of selectively impacting the expression of individual or a limited number of genes.

EXPERT OPINION

Modulation of G4 formation by specific ligands has been proposed as a powerful new tool to treat cancer through the control of oncogene expression. Actually, most of G4-binding small molecules seem to simultaneously target a range of gene promoter G4s, potentially influencing several critical driver genes in cancer, thus producing significant therapeutic benefits.

Tuning the ring strain effect in acridine derivatives on binding affinity with G-quadruplex-DNA: A computational and experimental study

Search for inhibitors to stabilize the telomeric G-quadruplex in order to deter telomerase activity is an active area of research. Inhibitors play an important role to initiate the tumor cell mortalization process. This work reports for the first time of acridine derivative with four membered ammonium rings at the side chain to surpass the binding ability against BRACO-19 with G-quadruplex-DNA. It is known in the literature that acridine based molecule BRACO-19 can effectively bind with G-quadruplex-DNA. The computational study performed in this study revealed that the binding ability of acridine based molecule can be augmented with subtle variation in the molecular structure of the drug like candidates. Steered molecular dynamics (SMD) performed with the acridine derivatives and G-quadruplex DNA showed the importance of ring strain to the side chain of those ligand molecules. The rupture force analysis, hydrogen bonding interactions and the calculated free energies in MM-PBSA method suggest that ligand 3 is superior than that of BRACO-19. The synthesized ligand 3 and BRACO-19 showed the binding constants obtained from ITC measurements are 4 × 10⁶ mol^-1 and 2.6 × 10⁶, which corroborates the computational findings.

The Consequences of Overlapping G-Quadruplexes and i-Motifs in the Platelet-Derived Growth Factor Receptor β Core Promoter Nuclease Hypersensitive Element Can Explain the Unexpected Effects of Mutations and Provide Opportunities for Selective Targeting of Both Structures by Small Molecules To Downregulate Gene Expression

The platelet-derived growth factor receptor β (PDGFR-β) signaling pathway is a validated and important target for the treatment of certain malignant and nonmalignant pathologies. We previously identified a G-quadruplex-forming nuclease hypersensitive element (NHE) in the human PDGFR-β promoter that putatively forms four overlapping G-quadruplexes. Therefore, we further investigated the structures and biological roles of the G-quadruplexes and i-motifs in the PDGFR-β NHE with the ultimate goal of demonstrating an alternate and effective strategy for molecularly targeting the PDGFR-β pathway. Significantly, we show that the primary G-quadruplex receptor for repression of PDGFR-β is the 3'-end G-quadruplex, which has a GGA sequence at the 3'-end. Mutation studies using luciferase reporter plasmids highlight a novel set of G-quadruplex point mutations, some of which seem to provide conflicting results on effects on gene expression, prompting further investigation into the effect of these mutations on the i-motif-forming strand. Herein we characterize the formation of an equilibrium between at least two different i-motifs from the cytosine-rich (C-rich) sequence of the PDGFR-β NHE. The apparently conflicting mutation results can be rationalized if we take into account the single base point mutation made in a critical cytosine run in the PDGFR-β NHE that dramatically affects the equilibrium of i-motifs formed from this sequence. We identified a group of ellipticines that targets the G-quadruplexes in the PDGFR-β promoter, and from this series of compounds, we selected the ellipticine analog GSA1129, which selectively targets the 3'-end G-quadruplex, to shift the dynamic equilibrium in the full-length sequence to favor this structure. We also identified a benzothiophene-2-carboxamide (NSC309874) as a PDGFR-β i-motif-interactive compound. In vitro, GSA1129 and NSC309874 downregulate PDGFR-β promoter activity and transcript in the neuroblastoma cell line SK-N-SH at subcytotoxic cell concentrations. GSA1129 also inhibits PDGFR-β-driven cell proliferation and migration. With an established preclinical murine model of acute lung injury, we demonstrate that GSA1129 attenuates endotoxin-mediated acute lung inflammation. Our studies underscore the importance of considering the effects of point mutations on structure formation from the G- and C-rich sequences and provide further evidence for the involvement of both strands and associated structures in the control of gene expression.

Quantum mechanical calculations unveil the structure and properties of the absorbing and emitting excited electronic states of guanine quadruplex

Herein, a full quantum mechanical study, in solution, of several models of guanine-quadruplex helices, both parallel and antiparallel, containing up to eight guanine residues, in their electronic excited state is reported. By exploiting TD-DFT calculations and including solvent effects by the polarizable continuum model, we provide the first atomistic description of the processes triggered by the absorption of UV light, reproducing and assigning the experimental optical and electronic circular dichroism spectra. The absorbing excited states are delocalized over multiple bases, whereas emission involves a stacked guanine dimer or a monomer. Several states, with a varying degree of localization and charge-transfer character, rule the photoexcited dynamics, which are deeply affected by the quadruplex topology. The lowest excited-state minimum for parallel quadruplex is an asymmetric excimer involving two stacked guanines, with a small charge transfer character, whereas for the anti-parallel structure, with the same topology of the thrombin binding aptamer, it is a fully symmetric excimer, characterized by a strong decrease of the stacking distance. A monomer-like decay path is the most relevant nonradiative decay pathway. Insights on the effect of the ions (K(+) or Na(+)) on the excited state decay are also provided.

Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein

Unlike DNA duplexes that release water upon interaction with protein, the binding of DNA G-quadruplex of the thrombin-binding aptamer (TBA) to thrombin takes up water. Here, to reveal the mechanism of water uptake, we designed four mutants of TBA (ΔT3, ΔT7, ΔT9, ΔT12), in which thymine residues (T3, T7, T9 and T12) were deleted from the loop regions of TBA G-quadruplex. For the mutants the thermodynamics and the osmolyte effects on the interactions with thrombin were investigated. The mutants ΔT3, ΔT9 and ΔT12 decreased the binding constants of the G-quadruplex to thrombin. Furthermore, an osmotic stress analysis indicated that the number of water molecules binding to the complex decreased in the mutants ΔT3 and ΔT9. The decrease in the binding affinity was related to loss of binding of the loop nucleotides to water molecules. Therefore, the interaction between loops of the G-quadruplex and water molecules contributed to the binding energy of G-quadruplex to protein. Our study suggests that water binding is essential for the binding of G-quadruplex to protein.

Synthesis of a dibromoperylene phosphoramidite building block and its incorporation at the 5' end of a G-quadruplex forming oligonucleotide: spectroscopic properties and structural studies of the resulting dibromoperylene conjugate

Previous studies indicate that some perylene bisimide derivatives can drive the assembly of DNA G-quadruplexes, thus suggesting the possible advantage in the adoption of perylene-conjugated G-rich oligonucleotides in biological and biotechnological applications. Nevertheless, the typical poor solubility of perylene bisimides strongly limits the number of suitable chemical strategies to prepare perylene-conjugated oligonucleotides. In order to overcome these difficulties, we employed the earlier described core twisted perylene derivatives possessing unique optical and electronic properties, besides good solubility in common solvents. As a first result, the large-scale synthesis of a new dibromoperylene derivative (PEOEBr) phosphoramidite building block is herein reported. Furthermore, the structural behavior of the conjugated PEOEBr-GGGTTAGGG (HTRp2) human telomeric repeat was investigated by using CD, UV, fluorescence, and gel electrophoresis techniques in desalted water and in K(+)- and Na(+)-containing buffers. We observed that the peculiar property of PEOEBr moieties to form dimers instead of extended aggregates drives the HTRp2 strands toward dimerization and mainly promotes the formation of quadruplex species having both the 5'-ends located at the same side of the structures. However, the counterions present in solutions (K(+) or Na(+)) as well as the strand concentration, also contribute to influence the topology and the stoichiometry of formed structures. Furthermore, unlike the unmodified sequence GGGTTAGGG (HTR2), HTRp2 strands quickly associate into G-quadruplexes even in desalted water, as assessed by CD experiments.

The evolving world of protein-G-quadruplex recognition: a medicinal chemist's perspective

The physiological and pharmacological role of nucleic acids structures folded into the non canonical G-quadruplex conformation have recently emerged. Their activities are targeted at vital cellular processes including telomere maintenance, regulation of transcription and processing of the pre-messenger or telomeric RNA. In addition, severe conditions like cancer, fragile X syndrome, Bloom syndrome, Werner syndrome and Fanconi anemia J are related to genomic defects that involve G-quadruplex forming sequences. In this connection G-quadruplex recognition and processing by nucleic acid directed proteins and enzymes represents a key event to activate or deactivate physiological or pathological pathways. In this review we examine protein-G-quadruplex recognition in physiologically significant conditions and discuss how to possibly exploit the interactions' selectivity for targeted therapeutic intervention.

Thin multilayer films and microcapsules containing DNA quadruplex motifs

The assembly of multifunctional nanostructures bearing G-quadruplex motifs broadens the prospects of using G-quadruplexes as therapeutic carriers. Herein, we report the synthesis and characterization of an oligodeoxyguanosine, G15-mer polymer conjugate. We demonstrate that G15-mer oligonucleotides grafted to a polymer chain preserve the ability to self-assemble into ordered structures. The G-quadruplex-polymer conjugates were assembled onto a surface via hybridization with 30-mer cytosine strands, C30-mer, using a layer-by-layer approach to form microcapsules. A mechanism for the sequential assembly of the multilayer films and microcapsules is presented. We further investigate the photophysical behavior of porphyrin TMPyP4 bound to multilayer-coated particles. This study shows that the multilayer films bear residual and functional quadruplex moieties that can be used to effectively bind therapeutic agents.

Formation of i-motif structure at neutral and slightly alkaline pH

It is well known that oligonucleotides containing tracts cytosines can form i-motif structures under acidic conditions (pH < 7). However, whether i-motif can be formed under normal physiological cellular conditions (pH 7.0-7.5) is yet no conclusive proof. In the present work, using circular dichroism (CD), UV absorption spectroscopies and native polyacrylamide gel electrophoresis (PAGE), we provided the compelling evidence for the formation of i-motif structures by four cytosine clusters, [C(3)TA(2)](3)C(3) (HT), [C(4)G](3)C(4)TA (RET), C(2)T(3)C(2)T(4)C(2)T(3)C(2) (CTC) and GC(2)GC(3)A(4)C(6)G (Rb), at neutral and slightly alkaline pH at 4 degrees C. Furthermore, for HT, we also supplied the evidence for the formation of i-motif structure by fluorescence resonance energy transfer (FRET) and investigated its folding kinetics. The formation time constants obtained by CD and fluorescence experiments are 214 and 493 s, respectively, indicating that HT can slowly form i-motif structure at pH 7.0 and 4 degrees C. This work implies that i-motif structures may possible form in vivo.

Differential inhibitory activities and stabilisation of DNA aptamers against the SARS coronavirus helicase

The helicase from severe acute respiratory syndrome coronavirus (SARS‐CoV) possesses NTPase, duplex RNA/DNA‐unwinding and RNA‐capping activities that are essential for viral replication and proliferation. Here, we have isolated DNA aptamers against the SARS‐CoV helicase from a combinatorial DNA library. These aptamers show two distinct classes of secondary structure, G‐quadruplex and non‐G‐quadruplex, as shown by circular dichroism and gel electrophoresis. All of the aptamers that were selected stimulated ATPase activity of the SARS‐CoV helicase with low‐nanomolar apparent K_m values. Intriguingly, only the non‐G‐quadruplex aptamers showed specific inhibition of helicase activities, whereas the G‐quadruplex aptamers did not inhibit helicase activities. The non‐G‐quadruplex aptamer with the strongest inhibitory potency was modified at the 3′‐end with biotin or inverted thymidine, and the modification increased its stability in serum, particularly for the inverted thymidine modification. Structural diversity in selection coupled to post‐selection stabilisation has provided new insights into the aptamers that were selected for a helicase target. These aptamers are being further developed to inhibit SARS‐CoV replication.