Cationic helicenes as selective G4 DNA binders and optical probes for cellular imaging

The important role that G-quadruplex DNA (G4 DNA) structures play in regulating biological processes is becoming widely recognised. These structures have also been proposed to be attractive drug targets. Therefore, there has been significant interest in developing small molecules that can selectively bind to G4 DNA over other topologies. In this paper we investigate the interaction between DNA and helical compounds (helicenes) based on a central carbocation trisubstituted with aromatic rings. We show that the non-planar structure of these helicenes results in a significantly reduced affinity for dsDNA when compared to their planar analogues, whilst maintaining a high affinity for G4 DNA. Additionally, the right- and left-handed enantiomers of one of these helicenes recognise the chiral DNA environments of G4 and dsDNA differently. We show that upon DNA binding the helicenes display a fluorescence switch-on effect, which we have successfully used for cellular imaging in live and fixed U2OS cells, staining mitochondria and the nucleus, respectively.

G-quadruplex DNA (G4 DNA) structures are selectively recognised by helical optical probes.     

A complementary chemical probe approach towards customized studies of G-quadruplex DNA structures in live cells

G-quadruplex (G4) DNA structures are implicated in central biological processes and are considered promising therapeutic targets because of their links to human diseases such as cancer. However, functional details of how, when, and why G4 DNA structures form in vivo are largely missing leaving a knowledge gap that requires tailored chemical biology studies in relevant live-cell model systems. Towards this end, we developed a synthetic platform to generate complementary chemical probes centered around one of the most effective and selective G4 stabilizing compounds, Phen-DC3. We used a structure-based design and substantial synthetic devlopments to equip Phen-DC3 with an amine in a position that does not interfere with G4 interactions. We next used this reactive handle to conjugate a BODIPY fluorophore to Phen-DC3. This generated a fluorescent derivative with retained G4 selectivity, G4 stabilization, and cellular effect that revealed the localization and function of Phen-DC3 in human cells. To increase cellular uptake, a second chemical probe with a conjugated cell-penetrating peptide was prepared using the same amine-substituted Phen-DC3 derivative. The cell-penetrating peptide conjugation, while retaining G4 selectivity and stabilization, increased nuclear localization and cellular effects, showcasing the potential of this method to modulate and direct cellular uptake e.g. as delivery vehicles. The applied approach to generate multiple tailored biochemical tools based on the same core structure can thus be used to advance the studies of G4 biology to uncover molecular details and therapeutic approaches.

The development of an approach to generate multiple tailored biochemical tools based on the same core structure, Phen-DC3, to advance studies of G4 biology to uncover molecular details and therapeutic approaches.     

Phosphorus-ylides: powerful substituents for the stabilization of reactive main group compounds

Phosphorus ylides are 1,2-dipolar compounds with a negative charge on the carbon atom. This charge is stabilized by the neighbouring onium moiety, but can also be shifted towards other substituents thus making ylides strong π donor ligands and hence ideal substituents to stabilize reactive compounds such as cations and low-valent main group species. Furthermore, the donor strength and the steric properties can easily be tuned to meet different requirements for stabilizing reactive compounds and for tailoring the properties and reactivities of the main group element. Although the use of ylide substituents in main group chemistry is still in its infancy, the first examples of isolated compounds impressively demonstrate the potential of these ligands. This review summarizes the most important discoveries also in comparison to other substituents, thus outlining avenues for future research directions.

The application of ylide substituents as strong donor ligands for the stabilization of reactive main group compounds with unusual properties and reactivities is discussed.     

Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design

Carbasugars are structural mimics of naturally occurring carbohydrates that can interact with and inhibit enzymes involved in carbohydrate processing. In particular, carbasugars have attracted attention as inhibitors of glycoside hydrolases (GHs) and as therapeutic leads in several disease areas. However, it is unclear how the carbasugars are recognized and processed by GHs. Here, we report the synthesis of three carbasugar isotopologues and provide a detailed transition state (TS) analysis for the formation of the initial GH-carbasugar covalent intermediate, as well as for hydrolysis of this intermediate, using a combination of experimentally measured kinetic isotope effects and hybrid QM/MM calculations. We find that the α-galactosidase from Thermotoga maritima effectively stabilizes TS charge development on a remote C5-allylic center acting in concert with the reacting carbasugar, and catalysis proceeds via an exploded, or loose, S_N2 transition state with no discrete enzyme-bound cationic intermediate. We conclude that, in complement to what we know about the TS structures of enzyme-natural substrate complexes, knowledge of the TS structures of enzymes reacting with non-natural carbasugar substrates shows that GHs can stabilize a wider range of positively charged TS structures than previously thought. Furthermore, this enhanced understanding will enable the design of new carbasugar GH transition state analogues to be used as, for example, chemical biology tools and pharmaceutical lead compounds.

Positive charge stabilized on remote C5-allylic center with catalysis occurring via a loose S_N2 transition state.     

Using steric hindrance to manipulate and stabilize metal halide perovskites for optoelectronics

The chemical instability of metal halide perovskite materials can be ascribed to their unique properties of softness, in which the chemical bonding between metal halide octahedral frameworks and cations is the weak ionic and hydrogen bonding as in most perovskite structures. Therefore, various strategies have been developed to stabilize the cations and metal halide frameworks, which include incorporating additives, developing two-dimensional perovskites and perovskite nanocrystals, etc. Recently, the important role of utilizing steric hindrance for stabilizing and passivating perovskites has been demonstrated. In this perspective, we summarize the applications of steric hindrance in manipulating and stabilizing perovskites. We will also discuss how steric hindrance influences the fundamental kinetics of perovskite crystallization and film formation processes. The similarities and differences of the steric hindrance between perovskite solar cells and perovskite light emission diodes are also discussed. In all, utilizing steric hindrance is a promising strategy to manipulate and stabilize metal halide perovskites for optoelectronics.

Manipulation on steric hindrance can influence the fundamental kinetics of perovskite crystallization and film formation, therefore stabilizing and passivating perovskite structures, and promoting the commercialization of stable perovskite devices.     

N-Heterocyclic carbene–carbodiimide (NHC–CDI) betaine adducts: synthesis,characterization, properties,and applications

N-Heterocyclic carbenes (NHCs) are an important class of reactive organic molecules used as ligands, organocatalysts, and σ-donors in a variety of electroneutral ylide or betaine adducts with main-group compounds. An emerging class of betaine adducts made from the reaction of NHCs with carbodiimides (CDIs) form zwitterionic amidinate-like structures with tunable properties based on the highly modular NHC and CDI scaffolds. The adduct stability is controlled by the substituents on the CDI nitrogens, while the NHC substituents greatly affect the configuration of the adduct in the solid state. This Perspective is intended as a primer to these adducts, touching on their history, synthesis, characterization, and general properties. Despite the infancy of the field, NHC–CDI adducts have been applied as amidinate-type ligands for transition metals and nanoparticles, as junctions in zwitterionic polymers, and to stabilize distonic radical cations. These applications and potential future directions are discussed.

N-heterocyclic carbene-carbodiimide betaine adducts are zwitterionic amidinate-like structures with tunable properties that have applications as ligands, junctions in supramolecular polymers, and stabilizers for radical cations.     

Electrochemical oxidative decarboxylation and 1,2-aryl migration towards the synthesis of 1,2-diaryl ethers

Carboxylic acid compounds are important chemicals and are widely present in various natural products. They are not only nucleophiles, but also radical precursors. Classic transition-metal-catalyzed and photochemical decarboxylation have shown their excellent site selectivity in radical chemistry. However, electrochemical decarboxylation with a long history hasn''t got enough attention in recent years. In this work, the electrochemical oxidative decarboxylation and 1,2-aryl migration of 3,3-diarylpropionic acids have been introduced to construct C–O bonds with alcohols. Remarkably, this transformation can proceed smoothly without metal catalysts and external oxidants.

Carboxylic acid compounds are important chemicals and are widely present in various natural products. The conversion of carboxylic acids into valuable compounds is a promising field.     

Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes.

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.     

Iron porphyrin catalysed light driven C–H bond amination and alkene aziridination with organic azides

Visible light driven nitrene transfer and insertion reactions of organic azides are an attractive strategy for the design of C–N bond formation reactions under mild reaction conditions, the challenge being lack of selectivity as a free nitrene reactive intermediate is usually involved. Herein is described an iron(iii) porphyrin catalysed sp³ C–H amination and alkene aziridination with selectivity by using organic azides as the nitrogen source under blue LED light (469 nm) irradiation. The photochemical reactions display chemo- and regio-selectivity and are effective for the late-stage functionalization of natural and bioactive compounds with complexity. Mechanistic studies revealed that iron porphyrin plays a dual role as a photosensitizer and as a catalyst giving rise to a reactive iron–nitrene intermediate for subsequent C–N bond formation.

An iron(iii) porphyrin catalysed sp³ C–H amination and alkene aziridination with broad substrate scope under mild conditions is conducted, with selectivity through the use of organic azides as the nitrogen source under blue LED light irradiation.     

Bouncing off walls – widths of exit channels from shallow minima can dominate selectivity control

A selectivity model based on the widths of pathways to competing products, rather than barrier heights, is formulated for the butadiene + allyl cation reaction. This model was arrived at via analysis of stationary points, intrinsic reaction coordinates, potential energy surface shapes and direct dynamics trajectories, all determined using quantum chemical methods.

A selectivity model based on the widths of pathways to competing products, rather than barrier heights, is formulated for the butadiene + allyl cation reaction.     

Thionated organic compounds as emerging heavy-atom-free photodynamic therapy agents

This minireview focuses on recent progress in developing heavy-atom-free photosensitizers based on the thionation of nucleic acid derivatives and other biocompatible organic compounds for prospective applications in photodynamic therapy. Particular attention is given to the use of thionated nucleobase derivatives as “one-two punch” photodynamic agents. These versatile photosensitizers can act as “Trojan horses” upon metabolization into DNA and exposure to activating light. Their incorporation into cellular DNA increases their selectivity and photodynamic efficacy against highly proliferating skin cancer tumor cells, while simultaneously enabling the use of low irradiation doses both in the presence and in the absence of molecular oxygen. Also reviewed are their primary photochemical reactions, modes of action, and photosensitization mechanisms. New developments of emerging thionated organic photosensitizers absorbing visible and near-infrared radiation are highlighted. Future research directions, as well as, other prospective applications of heavy-atom-free, thionated photosensitizers are discussed.

This minireview focuses on recent progress in developing heavy-atom-free photosensitizers based on the thionation of nucleic acid derivatives and other biocompatible organic compounds for prospective applications in photodynamic therapy.     

Base-catalyzed aryl halide isomerization enables the 4-selective substitution of 3-bromopyridines

The base-catalyzed isomerization of simple aryl halides is presented and utilized to achieve the 4-selective etherification, hydroxylation and amination of 3-bromopyridines. Mechanistic studies support isomerization of 3-bromopyridines to 4-bromopyridines proceeds via pyridyne intermediates and that 4-substitution selectivity is driven by a facile aromatic substitution reaction. Useful features of a tandem aryl halide isomerization/selective interception approach to aromatic functionalization are demonstrated. Example benefits include the use of readily available and stable 3-bromopyridines in place of less available and stable 4-halogenated congeners and the ability to converge mixtures of 3- and 5-bromopyridines to a single 4-substituted product.

The base-catalyzed isomerization of aryl halides is described and applied to the tandem isomerization/4-substitution of 3-bromopyridines as a strategy for achieving unconventional selectivity in nucleophilic aromatic substitution reactions.     

Copper-mediated peptide arylation selective for the N-terminus

Polypeptides present remarkable selectivity challenges for chemical methods. Amino groups are ubiquitous in polypeptide structure, yet few paradigms exist for reactivity and selectivity in arylation of amine groups. This communication describes the utilization of boronic acid reagents bearing certain o-electron withdrawing groups for copper-mediated amine arylation of the N-terminus under mild conditions and primarily aqueous solvent. The method adds to the toolkit of boronic acid reagents for polypeptide modification under mild conditions in water that shows complete selectivity for the N-terminus in the presence of lysine side chains.

The discovery of unique Chan-Lam coupling reactivity of arylboronic acids containing an ortho-sulfonamide group allows site-specific tailoring of peptide structure.     

Rapid and ultrasensitive electrochemical detection of circulating tumor DNA by hybridization on the network of gold-coated magnetic nanoparticles

An accurate and robust method for quantifying the levels of circulating tumor DNA (ctDNA) is vital if this potential biomarker is to be used for the early diagnosis of cancer. The analysis of ctDNA presents unique challenges because of its short half-life and ultralow abundance in early stage cancers. Here we develop an ultrasensitive electrochemical biosensor for rapid detection of ctDNA in whole blood. The sensing of ctDNA is based on hybridization on a network of probe DNA modified gold-coated magnetic nanoparticles (DNA-Au@MNPs). This DNA-Au@MNPs biosensor can selectively detect short- and long-strand DNA targets. It has a broad dynamic range (2 aM to 20 nM) for 22 nucleotide DNA target with an ultralow detection limit of 3.3 aM. For 101 nucleotide ctDNA target, a dynamic range from 200 aM to 20 nM was achieved with a detection limit of 5 fM. This DNA-Au@MNPs based sensor provides a promising method to achieve 20 min response time and minimally invasive cancer early diagnosis.

This study introduces a new electrochemical sensing strategy for the rapid detection of circulating tumor DNA (ctDNA) from whole blood in combination with a network of DNA-Au@MNPs with high sensitivity and excellent selectivity.     

Actinide tetra-N-heterocyclic carbene ‘sandwiches’

Highly-symmetrical, thorium and uranium octakis-carbene ‘sandwich’ complexes have been prepared by ‘sandwiching’ the An(iv) cations between two anionic macrocyclic tetra-NHC ligands, one with sixteen atoms and the other with eighteen atoms. The complexes were characterized by a range of experimental methods and DFT calculations. X-ray crystallography confirms the geometry at the metal centre can be set by the size of the macrocyclic ring, leading to either square prismatic or square anti-prismatic shapes; the geometry of the latter is retained in solution, which also undergoes reversible, electrochemical one-electron oxidation or reduction for the uranium variant. DFT calculations reveal a frontier orbital picture that is similar to thorocene and uranocene, in which the NHC ligands show almost exclusively σ-donation to the metal without π-backbonding.

Highly-symmetrical, thorium and uranium octakis-carbene ‘sandwich’ complexes have been prepared by ‘sandwiching’ the An(iv) cations between two anionic macrocyclic tetra-NHC ligands, one with sixteen atoms and the other with eighteen atoms.     

Formyl-selective deuteration of aldehydes with D2O via synergistic organic and photoredox catalysis

Formyl-selective deuteration of aldehydes is of high interest for labeling purposes and for optimizing properties of drug candidates. Herein, we report a mild general method for formyl-selective deuterium labeling of aldehydes with D₂O, an inexpensive deuterium source, via a synergistic combination of light-driven, polyoxometalate-facilitated hydrogen atom transfer and thiol catalysis. This highly efficient, scalable reaction showed excellent deuterium incorporation, a broad substrate scope, and excellent functional group tolerance and selectivity and is therefore a practical method for late-stage modification of synthetic intermediates in medicinal chemistry and for generating libraries of deuterated compounds.

Formyl-selective deuteration of aldehydes with D₂O mediated by the synergistic combination of light-driven, polyoxometalate-facilitated HAT and thiol catalysis is reported.     

Expected and unexpected photoreactions of 9-(10-)substituted anthracene derivatives in cucurbit[n]uril hosts

By arranging substrates in a “reaction ready” state through noncovalent interactions, supramolecular nanoreactors/catalysts show high selectivity and/or rate acceleration features. Herein, we report the host–guest complexation of 9-(10-)substituted anthracene derivatives (G1–G3) with cucurbit[n]uril (CB[n], n = 8, 10), and the photoreactions of these derivatives in the presence of CB[n] hosts. Both CB[10] and CB[8] showed no obvious effects on the photoreaction of 9,10-disubstituted derivative G1. For G2 and G3, CB[10] operated as either a nanoreactor or catalyst (10%) for the photodimerization of two compounds with high selectivity and high yield. However, although CB[8] formed a 1 : 2 complex with G2, as also observed with CB[10], the photosolvolysis product (9-anthracenemethanol) was obtained quantitatively after photoirradiation of the CB[8]·2G2 complex. This unexpected photosolvolysis was rationalized by a plausible catalytic cycle in which anthracene acts as a photoremovable protecting group (PPG) and the carbonium ion intermediate is stabilized by CB[8].

The photodimerization of 9-substituted anthracene derivative was tremendously promoted by a catalytic amount of cucurbit[10]uril (CB[10]) in water. While CB[8] exclusively induced the photosolvolysis of the anthracene derivative.     

Structural trends in the dehydrogenation selectivity of palladium alloys

Alloying is well-known to improve the dehydrogenation selectivity of pure metals, but there remains considerable debate about the structural and electronic features of alloy surfaces that give rise to this behavior. To provide molecular-level insights into these effects, a series of Pd intermetallic alloy catalysts with Zn, Ga, In, Fe and Mn promoter elements was synthesized, and the structures were determined using in situ X-ray absorption spectroscopy (XAS) and synchrotron X-ray diffraction (XRD). The alloys all showed propane dehydrogenation turnover rates 5–8 times higher than monometallic Pd and selectivity to propylene of over 90%. Moreover, among the synthesized alloys, Pd₃M alloy structures were less olefin selective than PdM alloys which were, in turn, almost 100% selective to propylene. This selectivity improvement was interpreted by changes in the DFT-calculated binding energies and activation energies for C–C and C–H bond activation, which are ultimately influenced by perturbation of the most stable adsorption site and changes to the d-band density of states. Furthermore, transition state analysis showed that the C–C bond breaking reactions require 4-fold ensemble sites, which are suggested to be required for non-selective, alkane hydrogenolysis reactions. These sites, which are not present on alloys with PdM structures, could be formed in the Pd₃M alloy through substitution of one M atom with Pd, and this effect is suggested to be partially responsible for their slightly lower selectivity.

Alloying is well-known to improve the dehydrogenation selectivity of pure metals, but there remains considerable debate about the structural and electronic features of alloy surfaces that give rise to this behavior.     

FeII4L4 tetrahedron binds and aggregates DNA G-quadruplexes

Since the discovery of the G-quadruplex (G4) structure in telomeres in 1980s, studies have established the role it plays in various biological processes. Here we report binding between DNA G4 and a self-assembled tetrahedral metal-organic cage 1 and consequent formation of aggregates, whereby the cage protects the DNA G4 from cleavage by S1 nuclease. We monitor DNA–cage interaction using fluorescence spectroscopy, firstly by quenching of a fluorescent label appended to the 5′ end of G4. Secondly, we detect the decrease in fluorescence of the G4-selective dyes thioflavin-T and Zn-PPIX bound to various DNA G4 sequences following the addition of cage 1. Our results demonstrate that 1 interacts with a wide range of G4s. Moreover, gel electrophoresis, circular dichroism and dynamic light scattering measurements establish the binding of 1 to G4 and indicate the formation of aggregate structures. Finally, we find that DNA G4 contained in an aggregate of cage 1 is protected from cleavage by S1 nuclease.

We find Fe^II₄L₄ binds to G-quadruplex and forms aggregates. G-quadruplex in the aggregates is protected from digestion by S₁ nuclease.