Interaction of Metal Complexes with G‐Quadruplex DNA

Guanine‐rich sequences of DNA can assemble into tetrastranded structures known as G‐quadruplexes. It has been suggested that these secondary DNA structures could be involved in the regulation of several key biological processes. In the human genome, guanine‐rich sequences with the potential to form G‐quadruplexes exist in the telomere as well as in promoter regions of certain oncogenes. The identification of these sequences as novel targets for the development of anticancer drugs has sparked great interest in the design of molecules that can interact with quadruplex DNA. While most reported quadruplex DNA binders are based on purely organic templates, numerous metal complexes have more recently been shown to interact effectively with this DNA secondary structure. This Review provides an overview of the important roles that metal complexes can play as quadruplex DNA binding molecules, highlighting the unique properties metals can confer to these molecules.     

Identification of Compounds that Selectively Stabilize Specific G‐Quadruplex Structures by Using a Thioflavin T‐Displacement Assay as a Tool

Small molecules are used in the G‐quadruplex (G4) research field in vivo and in vitro, and there are increasing demands for ligands that selectively stabilize different G4 structures. Thioflavin T (ThT) emits an enhanced fluorescence signal when binding to G4 structures. Herein, we show that ThT can be competitively displaced by the binding of small molecules to G4 structures and develop a ThT‐displacement high‐throughput screening assay to find novel and selective G4‐binding compounds. We screened approximately 28 000 compounds by using three different G4 structures and identified eight novel G4 binders. Analysis of the structural conformation and stability of the G4 structures in presence of these compounds demonstrated that the four compounds enhance the thermal stabilization of the structures without affecting their structural conformation. In addition, all four compounds also increased the G4‐structure block of DNA synthesis by Taq DNA polymerase. Also, two of these compounds showed selectivity between certain Schizosaccharomyces pombe G4 structures, thus suggesting that these compounds or their analogues can be used as selective tools for G4 DNA studies.     

Using a Multi‐Shelled Hollow Metal–Organic Framework as a Host to Switch the Guest‐to‐Host and Guest‐to‐Guest Interactions

A bio‐inspired design of using metal–organic framework (MOF) microcrystals with well‐defined multi‐shelled hollow structures was used as a matrix to host multiple guests including molecules and nanoparticles at separated locations to form a hierarchical material, mimicking biological structures. The interactions such as energy transfer (ET) between different guests are regulated by precisely fixing them in the MOF shells or encapsulating them in the cavities between the MOF shells. The proof‐of‐concept design is demonstrated by hosting chromophore molecules including rhodamine 6G (R6G) and 7‐amino‐4‐(trifluoromethyl)coumarin (C‐151), as well as metal nanoparticles (Pd NPs) into the multi‐shelled hollow zeolitic imidazolate framework‐8 (ZIF‐8). We could selectively establish or diminish the guest‐to‐framework and guest‐to‐guest ET. This work provides a platform to construct complex multifunctional materials, especially those need precise separation control of multi‐components.     

Identification and X‐ray Co‐crystal Structure of a Small‐Molecule Activator of LFA‐1‐ICAM‐1 Binding

Stabilization of protein–protein interactions by small molecules is a concept with few examples reported to date. Herein we describe the identification and X‐ray co‐crystal structure determination of IBE‐667, an ICAM‐1 binding enhancer for LFA‐1. IBE‐667 was designed based on the SAR information obtained from an on‐bead screen of tagged one‐bead one‐compound combinatorial libraries by confocal nanoscanning and bead picking (CONA). Cellular assays demonstrate the activity of IBE‐667 in promoting the binding of LFA‐1 on activated immune cells to ICAM‐1.     

An Aggregating Amphiphilic Squaraine: A Light‐up Probe That Discriminates Parallel G‐Quadruplexes

G‐quadruplexes (G4s) are peculiar DNA or RNA tertiary structures that are involved in the regulation of many biological events within mammalian cells, bacteria, and viruses. Although their role as versatile therapeutic targets has been emphasized for 35 years, G4 selectivity over ubiquitous double‐stranded DNA/RNA, as well as G4 differentiation by small molecules, still remains challenging. Here, a new amphiphilic dicyanovinyl‐substituted squaraine, SQgl , is reported to act as an NIR fluorescent light‐up probe discriminating an extensive panel of parallel G4s while it is non‐fluorescent in the aggregated state. The squaraine can form an unconventional sandwich π‐complex binding two quadruplexes, which leads to a strongly fluorescent (Φ _F=0.61) supramolecular architecture. SQgl is highly selective against non‐quadruplex and non‐parallel G4 sequences without altering their topology, as desired for applications in selective in vivo high‐resolution imaging and theranostics.     

Luminescent Strategies for Label‐Free G‐Quadruplex‐Based Enzyme Activity Sensing

By catalyzing highly specific and tightly controlled chemical reactions, enzymes are essential to maintaining normal cellular physiology. However, aberrant enzymatic activity can be linked to the pathogenesis of various diseases. Therefore, the unusual activity of particular enzymes can represent testable biomarkers for the diagnosis or screening of certain diseases. In recent years, G‐quadruplex‐based platforms have attracted wide attention for the monitoring of enzymatic activities. In this Personal Account, we discuss our group's works on the development of G‐quadruplex‐based sensing system for enzyme activities by using mainly iridium(III) complexes as luminescent label‐free probes. These studies showcase the versatility of the G‐quadruplex for developing assays for a variety of different enzymes.     

A Redox‐Activated G‐Quadruplex DNA Binder Based on a Platinum(IV)–Salphen Complex

There has been increasing interest in the development of small molecules that can selectively bind to G‐quadruplex DNA structures. The latter have been associated with a number of key biological processes and therefore are proposed to be potential targets for drug development. Herein, we report the first example of a reduction‐activated G‐quadruplex DNA binder. We show that a new octahedral platinum(IV)–salphen complex does not interact with DNA in aqueous media at pH 7.4; however, upon addition of bioreductants such as ascorbic acid or glutathione, the compound is readily reduced to the corresponding square planar platinum(II) complex. In contrast to the parent platinum(IV) complex, the in situ generated platinum(II) complex has good affinity for G‐quadruplex DNA.     

X‐ray Crystallography in Open‐Framework Materials

Open‐framework materials, such as metal–organic frameworks (MOFs) and coordination polymers have been widely investigated for their gas adsorption and separation properties. However, recent studies have demonstrated that their highly crystalline structures can be used to periodically organize guest molecules and non‐structural metal compounds either within their pore voids or by anchoring to their framework architecture. Accordingly, the open framework can act as a matrix for isolating and elucidating the structures of these moieties by X‐ray diffraction. This concept has broad scope for development as an analytical tool where obtaining single crystals of a target molecule presents a significant challenge and it additionally offers potential for obtaining insights into chemically reactive species that can be stabilized within the pore network. However, the technique does have limitations and as yet a general experimental method has not been realized. Herein we focus on recent examples in which framework materials have been utilized as a scaffold for ordering molecules for analysis by diffraction methods and canvass areas for future exploration.     

An ESI‐MS and NMR Study of the Self‐Assembly of Guanosine Derivatives

The self‐assembly of guanosine (G) derivatives in the presence of alkali‐metal ions gives octameric or polymeric aggregates composed of stacked G quartets. This process is studied for some lipophilic G derivatives by means of ESI‐MS. The ESI‐MS results are discussed in the light of complementary information obtained from NMR and SANS (small‐angle neutron scattering) studies. ESI‐MS gives an excellent picture of the self‐assembly process and gives new information on the effect of different cations and anions on the dimensions of the assembled species, information that could not have been obtained with SANS and NMR alone.     

Green Metal‐Free Photochemical Hydroacylation of Unactivated Olefins

Direct alkylation of C(sp²)?H bonds to convert an aldehyde into a ketone is a notorious transformation, due to the laborious challenge of the formation of ketyl or acyl radicals. Herein, we report a green, cheap, metal‐free and efficient method for the hydroacylation of olefins in water. This photochemical protocol utilizes phenylglyoxylic acid, a commercially available small organic molecule, as the photoinitiator, water as the solvent and household fluorescent lamps as the irradiation source, leading to a broad substrate scope of products in moderate to good yields. A wide range of aromatic and aliphatic aldehydes, terminal and non‐terminal alkenes and pharmaceutically relevant molecules can be employed, without the need of directing groups and additives or metal catalysts.     

Platinum Group Metal Clusters: From Gas‐Phase Structures and Reactivities towards Model Catalysts

Transition‐metal clusters have long been proposed as model systems to study heterogeneous catalysts. In this Concept article we show how advanced spectroscopic techniques can be used to determine the structures of gas‐phase transition‐metal clusters and their complexes with small molecules. Combined with computational studies, this can help to develop an understanding of the reactivity of these catalytic models.     

Molecular Pom Poms from Self‐Assembling α,γ‐Cyclic Peptides

The hierarchical self‐assembly properties of a dimer‐forming cyclic peptide that bears a nicotinic acid moiety to form molecular pom‐pom‐like structures are described. This dimeric assembly self organizes into spherical structures that can encapsulate small organic molecules owing to its porosity and it can also facilitate metal deposition on its surface directed by the pyridine moiety.     

Structural Design Principle of Small‐Molecule Organic Semiconductors for Metal‐Free,Visible‐Light‐Promoted Photocatalysis

Herein, we report on the structural design principle of small‐molecule organic semiconductors as metal‐free, pure organic and visible light‐active photocatalysts. Two series of electron‐donor and acceptor‐type organic semiconductor molecules were synthesized to meet crucial requirements, such as 1) absorption range in the visible region, 2) sufficient photoredox potential, and 3) long lifetime of photogenerated excitons. The photocatalytic activity was demonstrated in the intermolecular C?H functionalization of electron‐rich heteroaromates with malonate derivatives. A mechanistic study of the light‐induced electron transport between the organic photocatalyst, substrate, and the sacrificial agent are described. With their tunable absorption range and defined energy‐band structure, the small‐molecule organic semiconductors could offer a new class of metal‐free and visible light‐active photocatalysts for chemical reactions.     

Gradient‐driven molecule construction: An inverse approach applied to the design of small‐molecule fixating catalysts

Rational design of molecules and materials usually requires extensive screening of molecular structures for the desired property. The inverse approach to deduce a structure for a predefined property would be highly desirable, but is, unfortunately, not well defined. However, feasible strategies for such an inverse design process may be successfully developed for specific purposes. We discuss options for calculating “jacket” potentials that fulfill a predefined target requirement—a concept that we recently introduced (Weymuth and Reiher, MRS Proceedings 2013, 1524, DOI:10.1557/opl.2012.1764). We consider the case of small‐molecule activating transition metal catalysts. As a target requirement we choose the vanishing geometry gradients on all atoms of a subsystem consisting of a metal center binding the small molecule to be activated. The jacket potential can be represented within a full quantum model or by a sequence of approximations of which a field of electrostatic point charges is the simplest. In a second step, the jacket potential needs to be replaced by a chemically viable chelate‐ligand structure for which the geometry gradients on all of its atoms are also required to vanish. To analyze the feasibility of this approach, we dissect a known dinitrogen‐fixating catalyst to study possible design strategies that must eventually produce the known catalyst. © 2014 Wiley Periodicals, Inc.     

Peptide‐Directed Binding for the Discovery of Modulators of α‐Helix‐Mediated Protein–Protein Interactions: Proof‐of‐Concept Studies with the Apoptosis Regulator Mcl‐1

Targeting PPIs with small molecules can be challenging owing to large, hydrophobic binding surfaces. Herein, we describe a strategy that exploits selective α‐helical PPIs, transferring these characteristics to small molecules. The proof of concept is demonstrated with the apoptosis regulator Mcl‐1, commonly exploited by cancers to avoid cell death. Peptide‐directed binding uses few synthetic transformations, requires the production of a small number of compounds, and generates a high percentage of hits. In this example, about 50 % of the small molecules prepared showed an IC₅₀ value of less than 100 μm, and approximately 25 % had IC₅₀ values below 1 μm to Mcl‐1. Compounds show selectivity for Mcl‐1 over other anti‐apoptotic proteins, possess cytotoxicity to cancer cell lines, and induce hallmarks of apoptosis. This approach represents a novel and economic process for the rapid discovery of new α‐helical PPI modulators.     

Magnetic Alignment of Polymer Macro‐Nanodiscs Enables Residual‐Dipolar‐Coupling‐Based High‐Resolution Structural Studies by NMR Spectroscopy

Experimentally measured residual dipolar couplings (RDCs) are highly valuable for atomic‐resolution structural and dynamic studies of molecular systems ranging from small molecules to large proteins by solution NMR spectroscopy. Here we demonstrate the first use of magnetic‐alignment behavior of lyotropic liquid‐crystalline polymer macro‐nanodiscs (>20 nm in diameter) as a novel alignment medium for the measurement of RDCs using high‐resolution NMR. The easy preparation of macro‐nanodiscs, their high stability against pH changes and the presence of divalent metal ions, and their high homogeneity make them an efficient tool to investigate a wide range of molecular systems including natural products, proteins, and RNA.     

Potential‐Induced Fine‐Tuning of the Enantioaffinity of Chiral Metal Phases

Concepts leading to single enantiomers of chiral molecules are of crucial importance for many applications, including pharmacology and biotechnology. Recently, mesoporous metal phases encoded with chiral information have been developed. Fine‐tuning of the enantioaffinity of such structures by imposing an electric potential is proposed, which can influence the electrostatic interactions between the chiral metal and the target enantiomer. This allows the binding affinity between the chiral metal and the target enantiomer to be increased, and thus, the discrimination between two enantiomers to be improved. The concept is illustrated by generating chiral encoded metals in a microfluidic channel by reduction of a platinum salt in the presence of a liquid crystal and l ‐tryptophan as a chiral model template. After removal of the template molecules, the modified microchannel retains a pronounced chiral character. The chiral recognition efficiency of the microchannel can be fine‐tuned by applying a suitable potential to the metal phase. This enables the separation of both components of a racemate flowing through the channel. The approach constitutes a promising and complementary strategy in the frame of chiral discrimination technologies.     

Sensitive Detection of Small Molecule–Protein Interactions on a Metal–Insulator–Metal Label‐Free Biosensing Platform

The need to develop label‐free biosensing devices that enable rapid analyses of interactions between small molecules/peptides and proteins for post‐genomic studies has increased significantly. We report a simple metal–insulator–metal (MIM) geometry for fabricating a highly sensitive detection platform for biosensing. MIM substrates consisting of an Au–PMMA–Ag nanolayer were extensively studied using both theoretical and experimental approaches. By monitoring reflectivity changes at the normal incidence angle, we observed molecular interactions as the thickness of the biolayer increased on the substrate surface. These interactions included the adsorption of various proteins (Mw=6–150 kD) and interactions between small molecules (Mw≤2 kD) and the immobilized proteins. The interaction of designed monosaccharide‐modified designed peptides with various lectins was also clearly detected. These interactions could not be detected by the conventional Au‐only substrate. Thus, the MIM approach affords a powerful label‐free biosensing device that will aid our understanding of protein interactions and recognition.