A Fragment-Based Approach for the Development of G-Quadruplex Ligands: Role of the Amidoxime Moiety

G-quadruplex (G4) nucleic acid structures have been reported to be involved in several human pathologies, including cancer, neurodegenerative disorders and infectious diseases; however, G4 targeting compounds still need implementation in terms of drug-like properties and selectivity in order to reach the clinical use. So far, G4 ligands have been mainly identified through high-throughput screening methods or design of molecules with pre-set features. Here, we describe the development of new heterocyclic ligands through a fragment-based drug discovery (FBDD) approach. The ligands were designed against the major G4 present in the long terminal repeat (LTR) promoter region of the human immunodeficiency virus-1 (HIV-1), the stabilization of which has been shown to suppress viral gene expression and replication. Our method is based on the generation of molecular fragment small libraries, screened against the target to further elaborate them into lead compounds. We screened 150 small molecules, composed by structurally and chemically different fragments, selected from commercially available and in-house compounds; synthetic elaboration yielded several G4 ligands and two final G4 binders, both embedding an amidoxime moiety; one of these two compounds showed preferential binding for the HIV-1 LTR G4. This work presents the discovery of a novel potential pharmacophore and highlights the possibility to apply a fragment-based approach to develop G4 ligands with unexpected chemical features

A Catalytic and Selective Scissoring Molecular Tool for Quadruplex Nucleic Acids

A copper complex embedded in the structure of a water-soluble naphthalene diimide has been designed to bind and cleave G-quadruplex DNA. We describe the properties of this ligand, including its catalytic activity in the generation of ROS. FRET melting, CD, NMR, gel sequencing, and mass spectrometry experiments highlight a unique and unexpected selectivity in cleaving G-quadruplex sequences. This selectivity relies both on the binding affinity and structural features of the targeted G-quadruplexes

Trifunctionalized Naphthalene Diimides and Dimeric Analogues as G-Quadruplex-Targeting Anticancer Agents Selected by Affinity Chromatography

A focused library of newly designed monomeric and dimeric naphthalene diimides (NDIs) was analyzed in its ability to recognize specific G-quadruplex (G4) structures discriminating duplex DNA. The best G4 ligands—according to an affinity chromatography-based screening method named G4-CPG—were tested on human cancer and healthy cells, inducing DNA damage at telomeres, and in parallel, showing selective antiproliferative activity on HeLa cancer cells with IC50 values in the low nanomolar range. CD and fluorescence spectroscopy studies allowed detailed investigation of the interaction in solution with different G4 and duplex DNA models of the most promising NDI of the series, as determined by combining the biophysical and biological assays’ data

G-Quadruplex DNA as a Target in Pathogenic Bacteria:Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action

[Image: see text] Guanidine DNA quadruplex (G4-DNA) structures convey a distinctive layer of epigenetic information that is critical for regulating key biological activities and processes as transcription, replication, and repair in living cells. The information regarding their role and use as therapeutic drug targets in bacteria is still scarce. Here, we tested the biological activity of a G4-DNA ligand library, based on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive and Gram-negative bacteria. For the best compound identified, NDI-10, a different action mechanism was described for Gram-positive or negative bacteria. This asymmetric activity profile could be related to the different prevalence of putative G4-DNA structures in each group, the influence that they can exert on gene expression, and the different roles of the G4 structures in these bacteria, which seem to promote transcription in Gram-positive bacteria and repress transcription in Gram-negatives

Manipulating Color Emission in 2D Hybrid Perovskites by Fine Tuning Halide Segregation: A Transparent Green Emitter.

Halide perovskite materials offer an ideal playground for easily tuning their color and, accordingly, the spectral range of their emitted light. In contrast to common procedures, this work demonstrates that halide substitution in Ruddlesden-Popper perovskites not only progressively modulates the bandgap, but it can also be a powerful tool to control the nanoscale phase segregation-by adjusting the halide ratio and therefore the spatial distribution of recombination centers. As a result, thin films of chloride-rich perovskite are engineered-which appear transparent to the human eye-with controlled tunable emission in the green. This is due to a rational halide substitution with iodide or bromide leading to a spatial distribution of phases where the minor component is responsible for the tunable emission, as identified by combined hyperspectral photoluminescence imaging and elemental mapping. This work paves the way for the next generation of highly tunable transparent emissive materials, which can be used as light-emitting pixels in advanced and low-cost optoelectronics

Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis

Cerebellar Ataxia, Neuropathy and Vestibular Areflexia Syndrome (CANVAS) is an autosomal recessive neurodegenerative disease, usually caused by biallelic AAGGG repeat expansions in RFC1. In this study, we leveraged whole genome sequencing (WGS) data from nearly 10,000 individuals recruited within the Genomics England sequencing project to investigate the normal and pathogenic variation of the RFC1 repeat. We identified three novel repeat motifs, AGGGC (n=6 from 5 families), AAGGC (n=2 from 1 family), AGAGG (n=1), associated with CANVAS in the homozygous or compound heterozygous state with the common pathogenic AAGGG expansion. While AAAAG, AAAGGG and AAGAG expansions appear to be benign, here we show a pathogenic role for large AAAGG repeat configuration expansions (n=5). Long read sequencing was used to fully characterise the entire repeat sequence and revealed a pure AGGGC expansion in six patients, whereas the other patients presented complex motifs with AAGGG or AAAGG interruptions. All pathogenic motifs seem to have arisen from a common haplotype and are predicted to form highly stable G quadruplexes, which have been previously demonstrated to affect gene transcription in other conditions. The assessment of these novel configurations is warranted in CANVAS patients with negative or inconclusive genetic testing. Particular attention should be paid to carriers of compound AAGGG/AAAGG expansions, since the AAAGG motif when very large (>500 repeats) or in the presence of AAGGG interruptions. Accurate sizing and full sequencing of the satellite repeat with long read is recommended in clinically selected cases, in order to achieve an accurate molecular diagnosis and counsel patients and their families

Apolipoprotein E in Alzheimer’s Disease

The pathophysiology of Alzheimer’s disease (AD) is related with the ongoing deterioration of brain lipid homeostasis, in which the cholesterol transporter apolipoprotein E (APOE) plays a key role. Plasma protein APOE might be additionally associated with AD due to its capability to bind the amyloid protein. There are three principal isoforms: APOE2, APOE3 and APOE4, encoded by three different alleles (ε2, ε3, ε4). Among them, APOE4 is recognized as the toxic form involved in AD development and progression. In fact, the presence of the ε4 allele correlates to an increase of about three times in the risk of developing the disease in late onset forms, both familiar and sporadic. For this reason, APOE4 has been often highlighted as a promising therapeutic target. Nevertheless, recent studies also suggest that the reduction of APOE protein levels, regardless of the isoform present, might be beneficial to deal with AD progression. Herein we report a brief overview of the proposed roles of APOE and in particular of ApoE4 in the insurgence and development of AD. In particular, its intervention in amyloid-β dependent and independent processes are examined. New therapeutic approaches for AD exploiting APOE as a target are finally discussed

Groundbreaking Anticancer Activity of Highly Diversified Oxadiazole Scaffolds

Nowadays, an increasing number of heterocyclic-based drugs found application in medicinal chemistry and, in particular, as anticancer agents. In this context, oxadiazoles-five-membered aromatic rings-emerged for their interesting biological properties. Modification of oxadiazole scaffolds represents a valid strategy to increase their anticancer activity, especially on 1,2,4 and 1,3,4 regioisomers. In the last years, an increasing number of oxadiazole derivatives, with remarkable cytotoxicity for several tumor lines, were identified. Structural modifications, that ensure higher cytotoxicity towards malignant cells, represent a solid starting point in the development of novel oxadiazole-based drugs. To increase the specificity of this strategy, outstanding oxadiazole scaffolds have been designed to selectively interact with biological targets, including enzymes, globular proteins, and nucleic acids, showing more promising antitumor effects. In the present work, we aim to provide a comprehensive overview of the anticancer activity of these heterocycles, describing their effect on different targets and highlighting how their structural versatility has been exploited to modulate their biological properties

Synthesis of tetrazole- and imidazole-based compounds: prophetic molecules made real for biological studies

The synthesis of tetrazole- and imidazole-based derivatives has been achieved via sulfur nucleophilic ringopening of 2-oxiranyl-alcohols or chlorides. The derivatives obtained may represent interesting new chemical tools to investigate biological functions and in particular the mitochondrial molecular chaperone TRAP1. The results are discussed in the light of the availability of these molecules according to the proposed synthetic procedures

Naphthalene diimides as multimodal G-quadruplex-selective ligands

G-quadruplexes are four-stranded nucleic acids structures that can form in guanine-rich sequences. Following the observation that G-quadruplexes are particularly abundant in genomic regions related to cancer, such as telomeres and oncogenes promoters, several G-quadruplex-binding molecules have been developed for therapeutic purposes. Among them, naphthalene diimide derivatives have reported versatility, consistent selectivity and high affinity toward the G-quadruplex structures. In this review, we present the chemical features, synthesis and peculiar optoelectronic properties (absorption, emission, redox) that make naphtalene diimides so versatile for biomedical applications. We present the latest developments on naphthalene diimides as G-quadruplex ligands, focusing on their ability to bind G-quadruplexes at telomeres and oncogene promoters with consequent anticancer activity. Their different binding modes (reversible versus irreversible/covalent) towards G-quadruplexes and their additional use as antimicrobial agents are also presented and discussed