Characterization of G‐Quadruplex/Hairpin Transitions of RNAs by 19F NMR Spectroscopy

2′‐O‐[(4‐Trifluoromethyl‐triazol‐1‐yl)methyl] reporter groups have been incorporated into guanosine‐rich RNA models (including a known bistable Qd/Hp RNA and two G‐rich regions of mRNA of human prion protein, PrP) and applied for the ¹⁹F NMR spectroscopic characterization of plausible G‐quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF₃‐labeled RNAs, phosphoramidite building blocks of 2′‐O‐[(4‐CF₃‐triazol‐1‐yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid‐phase RNA synthesis. The obtained ¹⁹F NMR spectra supported the usual characterization data (obtained by UV‐ and CD‐melting profiles and by ¹H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the ¹⁹F NMR signals. For a well‐behaved Qd/Hp transition, thermodynamic parameters could be extracted.     

Recent Developments in Small-Molecule Ligands of Medicinal Relevance for Harnessing the Anticancer Potential of G-Quadruplexes

G-quadruplexes, a family of tetraplex helical nucleic acid topologies, have emerged in recent years as novel targets, with untapped potential for anticancer research. Their potential stems from the fact that G-quadruplexes occur in functionally-important regions of the human genome, such as the telomere tandem sequences, several proto-oncogene promoters, other regulatory regions and sequences of DNA (e.g., rDNA), as well as in mRNAs encoding for proteins with roles in tumorigenesis. Modulation of G-quadruplexes, via interaction with high-affinity ligands, leads to their stabilization, with numerous observed anticancer effects. Despite the fact that only a few lead compounds for G-quadruplex modulation have progressed to clinical trials so far, recent advancements in the field now create conditions that foster further development of drug candidates. This review highlights biological processes through which G-quadruplexes can exert their anticancer effects and describes, via selected case studies, progress of the last few years on the development of efficient and drug-like G-quadruplex-targeted ligands, intended to harness the anticancer potential offered by G-quadruplexes. The review finally provides a critical discussion of perceived challenges and limitations that have previously hampered the progression of G-quadruplex-targeted lead compounds to clinical trials, concluding with an optimistic future outlook.     

Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay

G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.     

A Light-Triggerable Nanoparticle Library for the Controlled Release of Non-Coding RNAs

RNA-based therapies offer a wide range of therapeutic interventions including the treatment of skin diseases; however, the strategies to efficiently deliver these biomolecules are still limited due to obstacles related to the cellular uptake and cytoplasmic delivery. Herein, we report the synthesis of a triggerable polymeric nanoparticle (NP) library composed of 160 formulations, presenting physico-chemical diversity and differential responsiveness to light. Six formulations were more efficient (up to 500 %) than commercially available lipofectamine in gene-knockdown activity. These formulations showed differential internalization by skin cells and the endosomal escape was rapid (minutes range). The NPs were effective in the release of siRNA and miRNA. Acute skin wounds treated with the top hit NP complexed with miRNA-150-5p healed faster than wounds treated with scrambled miRNA. Light-activatable NPs offer a new strategy to topically deliver non-coding RNAs.     

Benzene and Its Derivatives as Bridging Ligands in Transition-Metal Complexes

Transition-metal complexes in which two or more metal atoms are bridged by one or more arene ligands led a shadowy existence in comparison to the extensive class of mononuclear arene complexes. Arene bridges can occur in a variety of coordination modes and with almost all of the transition–metal elements of the periodic table. Nowhere else are found so many forms of distorted and bent arene rings. The binuclear compounds can be divided into two classes: adducts which show relatively weak metal–arene bonding and complexes which show strong arene–metal interaction. Most of the adducts are in equilibrium with mononuclear complexes in solution or are only stable in the solid state (often as polymers). In both classes syn and anti coordination occurs; their geometries show a wide variation between the extreme cases of η¹ : η¹-bridge and η⁶ : η⁶-triple-decker structure. Metal surfaces with chemisorbed arenes can be seen as a form of multinuclear arene–metal complexes. On transition-metal surfaces, benzene can be bonded to one, two, or four surface atoms. Molecular clusters with face-capping arene ligands that are bonded to three metal atoms have until now mainly been limited to two classes. The arenes bound to {(CO)₃M}₃ (M = Ru, Os) or (CpCo)₃ clusters as μ₃-η² : η² : η² ligands show only a weak trigonal distortion towards a Kekulé structure. Detailed investigations of the molecular structure and ligand dynamics of [(CpCo)₃(μ₃-arene)] complexes considerably help the understanding of the bonding of arenes to metal clusters and to metal surfaces.     

Sulfur Atoms as Ligands in Metal Complexes

The types of sulfur bonding—as sulfane or sulfide—encountered in the molecules of maingroup elements are almost unknown in the chemistry of metal complexes, where the sulfur atoms function instead as two-electron donors by bridging two metal atoms, as four-electron donors by bridging three or four metal atoms, or as six-electron donors by incorporation between four metal atoms. In such complexes, the metal-metal bond can be modified over a wide range by chemical or electrochemical variation of the number of electrons present. The readiness with which polynuclear complexes containing metals and sulfur undergo redox reactions is also utilized by Nature in the active sites of some redox proteins.     

Sulfur Oxides as Ligands in Coordination Compounds

Donor molecules undergo dramatic changes in their chemical properties on coordination to a transition-metal atom. Highly reactive species can be trapped and studied as ligands. Conversely, stable compounds can be activated to undergo novel reactions. Sulfur dioxide complexes have generally been studied from a structural viewpoint, their reactivity having been somewhat neglected. The unstable sulfur oxides SO, S₂O, and S₂O₂ are still often regarded as laboratory curiosities. Their successful stabilization in transition-metal complexes has now made them accessible to detailed study, in the course of which many relationships to the chemistry of SO₂ complexes have become apparent.     

A Light‐Triggerable Nanoparticle Library for the Controlled Release of Non‐Coding RNAs

RNA‐based therapies offer a wide range of therapeutic interventions including the treatment of skin diseases; however, the strategies to efficiently deliver these biomolecules are still limited due to obstacles related to the cellular uptake and cytoplasmic delivery. Herein, we report the synthesis of a triggerable polymeric nanoparticle (NP) library composed of 160 formulations, presenting physico‐chemical diversity and differential responsiveness to light. Six formulations were more efficient (up to 500 %) than commercially available lipofectamine in gene‐knockdown activity. These formulations showed differential internalization by skin cells and the endosomal escape was rapid (minutes range). The NPs were effective in the release of siRNA and miRNA. Acute skin wounds treated with the top hit NP complexed with miRNA‐150‐5p healed faster than wounds treated with scrambled miRNA. Light‐activatable NPs offer a new strategy to topically deliver non‐coding RNAs.     

Kinetic Target-Guided Synthesis of Small-Molecule G-Quadruplex Stabilizers

The formation of a G-quadruplex motif in the promoter region of the c-MYC protooncogene prevents its expression. Accordingly, G-quadruplex stabilization by a suitable ligand may be a viable approach for anticancer therapy. In our study, we used the 4-(4-methylpiperazin-1-yl)aniline molecule, previously identified as a fragment library screen hit, as a template for the SAR-guided design of a new small library of clickable fragments and subjected them to click reactions, including kinetic target-guided synthesis in the presence of a G-quadruplex forming oligonucleotide Pu24. We tested the clickable fragments and products of click reactions for their G-quadruplex stabilizing activity and determined their mode of binding to the c-MYC G-quadruplex by NMR spectroscopy. The enhanced stabilizing potency of click products in biology assays (FRET, Polymerase extension assay) matched the increased yields of in situ click reactions. In conclusion, we identified the newly synthesized click products of bis-amino derivatives of 4-(4-methylpiperazin-1-yl)aniline as potent stabilizers of c-MYC G-quadruplex, and their further evolution may lead to the development of an efficient tool for cancer treatment.     

Inorganic Esters of Ethylene Glycol as Macrocyclic Ligands

Six different inorganic esters of ethylene glycol: B(OR)₃, P(OR)₃, OS(OR)₂, OP(OR)₃, OPH(OR)₂ and As(OR)₃, where R = CH₂CH₂OCH₃ were obtained. Their structures were studied by multinuclear NMR. These compounds can complex metal cations and behave like macrocyclic ligands. The influence of metal cation complexation on spectra were investigated by ¹, ¹³C, ¹⁷O, ¹¹B, ⁷Li, ⁸⁷Rb and ³¹P NMR.     

Substituted Bisphosphanylamines as Ligands in Gold(I) Chemistry – Synthesis and Structures

Dimethyl 5‐aminoisophthalate, which is a building block of amino‐substituted tetralactam macrocycles, was used as ligand in gold(I) chemistry to form model complexes for macrocyclic gold compounds. Reaction of dimethyl 5‐aminoisophthalate with chlorodiphenylphosphine gave the diphosphine compound dimethyl 5‐[N,N‐bis(diphenylphosphanyl)amino]isophthalate (dmbpaip). This compound can further be reacted with [AuCl(tht)] (tht = tetrahydrothiophene) to give the dinuclear complex [Au₂Cl₂(dmbpaip)]. In contrast, treatment of dmbpaip with [Au(tht)₂]ClO₄ resulted in the ionic compound [Au₂(dmbpaip)₂](ClO₄)₂ in which the cation forms an eight‐membered Au₂P₄N₂ heterocycle. In both gold(I) compounds Au···Au interactions are observed. All new compounds were characterized by single‐crystal X‐ray diffraction.     

Phosphinothiolates as Ligands for Polyhydrido Copper Nanoclusters

The reaction of [CuI(HSC₆H₄PPh₂)]₂ with NaBH₄ in CH₂Cl₂/EtOH led to air‐ and moisture‐stable copper hydride nanoparticles (CuNPs) containing phosphinothiolates as new ligands, one of which was isolated by crystallization. The X‐ray crystal structure of [Cu₁₈H₇L₁₀I] (L=^?S(C₆H₄)PPh₂) shows unprecedented features in its 28‐atom framework (18 Cu and 10 S atoms). Seven hydrogen atoms, in hydride form, are needed for charge balance and were located by density functional theory methods. H₂ was released from the copper hydride nanoparticles by thermolysis and visible light irradiation.     

The Coordination Chemistry of Multidentate Isocyanide Ligands

In spite of the excellent ligation properties of isocyanides, until a few years ago there was only a small number of known multidentate ligands of this type. One of the reasons for this lack of interest, when compared to monodentate isocyanides, was the linear arrangement of the M? C?N? R group, which usually inhibits the formation of mononuclear chelate complexes and leads to the formation of multinuclear or polymeric metal complexes. In these, the multidentate ligand acts in a monodentate fashion towards each metal atom. Only recently has a series of polyisocyanides with large ligand backbones been synthesized successfully. Bidentate isocyanides can bridge two metal atoms or react to give chelates with only one metal center. Tripodal ligands form mono- or binuclear complexes, in which the largest organometallic rings observed to date occur (up to 36 atoms). This class of ligands promises to be interesting for the synthesis of stable, diagnostically important technetium complexes of the type [Tc(CNR) ₆ ]⁺. There also appear to be applications for tripodal isocyanides in catalysis. A facial, chiral Cr(CNR^*)₃ unit might be able to catalyze the hydrogenation or isomerization of prochiral double bonds. It is even possible to bind triisocyanides with suitable backbones to carbonyl trimetal clusters, thereby stabilizing them, or making selective cluster formation possible. Coordinated isocyanides can be transformed readily into carbene ligands, which, in the future, could lead to complexes with polycarbene ligation.     

Alkoxydiaminophosphine Ligands as Surrogates of NHCs in Copper Catalysis

A family of phosphine ligands containing a five-membered ring similar to the popular N-heterocyclic carbene ligands and an alkoxy third substituent has been developed. These alkoxydiaminophosphine ligands (ADAP) can be generated in one pot and reacted with a copper(I) source leading to the high yield isolation of complexes [(ADAP)CuX]₂ (X=Cl, Br). The dinuclear nature of these compounds has been established by means of X-ray studies and DOSY experiments. A screening of the catalytic properties of these complexes toward carbene-transfer reactions from diazocompounds to C−H bonds (alkane, arene), olefins or N−H bonds, as well as in CuAAC or nitrene transfer reactions have shown a performance at least similar, if not better, than their (NHC)CuCl analogues, opening a new window in copper catalysis with these readily tunable ADAP ligands.