Molecular Recognition of a Three-Way DNA Junction by a Metallosupramolecular Helicate

Structural Optimization of Azacryptands for Targeting Three-Way DNA Junctions

Transient melting of the duplex-DNA (B-DNA) during DNA transactions allows repeated sequences to fold into non-B-DNA structures, including DNA junctions and G-quadruplexes. These noncanonical structures can act as impediments to DNA polymerase progression along the duplex, thereby triggering DNA damage and ultimately jeopardizing genomic stability. Their stabilization by ad hoc ligands is currently being explored as a putative anticancer strategy since it might represent an efficient way to inflict toxic DNA damage specifically to rapidly dividing cancer cells. The relevance of this strategy is only emerging for three-way DNA junctions (TWJs) and, to date, no molecule has been recognized as a reference TWJ ligand, featuring both high affinity and selectivity. Herein, we characterize such reference ligands through a combination of in vitro techniques comprising affinity and selectivity assays (competitive FRET-melting and TWJ Screen assays), functional tests (qPCR and Taq stop assays) and structural analyses (molecular dynamics and NMR investigations). We identify novel azacryptands TrisNP-amphi and TrisNP-ana as the most promising ligands, interacting with TWJs with high affinity and selectivity. These ligands represent new molecular tools to investigate the cellular roles of TWJs and explore how they can be exploited in innovative anticancer therapies.

Interaction of dinuclear Co(III) cylinders with higher-order DNA structures

Alternative DNA structures play critical roles in fundamental biological processes linked to human diseases. Thus, targeting and stabilizing these structures by specific ligands could affect the progression of cancer and other diseases. Here, we describe, using methods of molecular biophysics, the interactions of two oxidatively locked [Co2L3]6+ cylinders, rac-2 and meso-1, with diverse alternative DNA structures, such as junctions, G quadruplexes, and bulges. This study was motivated by earlier results demonstrating that both Co(III) cylinders exhibit potent and selective activity against cancer cells, accumulate in the nucleus of cancer cells, and prove to be efficient DNA binders. The results show that the bigger cylinder rac-2 stabilizes all DNA structures, while the smaller cylinder meso-1 stabilizes just the Y-shaped three-way junctions. Collectively, the results of this study suggest that the stabilization of alternative DNA structures by Co(III) cylinders investigated in this work might contribute to the mechanism of their biological activity.

Schiff bases and their metal complexes to target and overcome (multidrug) resistance in cancer

Overcoming multidrug resistance (MDR) is one of the major challenges in cancer therapy. In this respect, Schiff base-related compounds (bearing a R1R2CNR3 bond) gained high interest during the past decades. Schiff bases are considered privileged ligands for various reasons, including the easiness of their preparation and the possibility to form complexes with almost all transition metal ions. Schiff bases and their metal complexes exhibit many types of biological activities and are used for the treatment and diagnosis of various diseases. Until now, 13 Schiff bases have been investigated in clinical trials for cancer treatment and hypoxia imaging. This review represents the first collection of Schiff bases and their complexes which demonstrated MDR-reversal activity. The areas of drug resistance covered in this article involve: 1) Modulation of ABC transporter function, 2) Targeting lysosomal ABCB1 overexpression, 3) Circumvention of ABC transporter-mediated drug efflux by alternative routes of drug uptake, 4) Selective activity against MDR cancer models (collateral sensitivity), 5) Targeting GSH-detoxifying systems, 6) Overcoming apoptosis resistance by inducing necrosis and paraptosis, 7) Reactivation of mutated p53, 8) Restoration of sensitivity to DNA-damaging anticancer therapy, and 9) Overcoming drug resistance through modulation of the immune system. Through this approach, we would like to draw attention to Schiff bases and their metal complexes representing highly interesting anticancer drug candidates with the ability to overcome MDR.

A copper(ii) peptide helicate selectively cleaves DNA replication foci in mammalian cells

The use of copper-based artificial nucleases as potential anticancer agents has been hampered by their poor selectivity in the oxidative DNA cleavage process. An alternative strategy to solve this problem is to design systems capable of selectively damaging noncanonical DNA structures that play crucial roles in the cell cycle. We designed an oligocationic CuII peptide helicate that selectively binds and cleaves DNA three-way junctions (3WJs) and induces oxidative DNA damage via a ROS-mediated pathway both in vitro and in cellulo, specifically at DNA replication foci of the cell nucleus, where this DNA structure is transiently generated. To our knowledge, this is the first example of a targeted chemical nuclease that can discriminate with high selectivity 3WJs from other forms of DNA both in vitro and in mammalian cells. Since the DNA replication process is deregulated in cancer cells, this approach may pave the way for the development of a new class of anticancer agents based on copper-based artificial nucleases.

Analysis of non-canonical three- and four-way DNA junctions

The development of compounds that can selectively bind with non-canonical DNA structures has expanded in recent years. Junction DNA, including three-way junctions (3WJs) and four-way Holliday junctions (HJs), offer an intriguing target for developmental therapeutics as both 3WJs and HJs are involved in DNA replication and repair processes. However, there are a limited number of assays available for the analysis of junction DNA binding. Here, we describe the design and execution of multiplex fluorescent polyacrylamide gel electrophoresis (PAGE) and microscale thermophoresis (MST) assays that enable evaluation of junction-binding compounds. Two well characterised junction-binding compounds-a C6 linked bis-acridine ligand and an iron(II)-bound peptide helicate, which recognise HJs and 3WJs, respectively-were employed as probes for both MST and PAGE experiments. The multiplex PAGE assay expands beyond previously reported fluorescent PAGE as it uses four individual fluorophores that can be combined to visualise single-strands, pseudo-duplexes, and junction DNA present during 3WJ and HJ formation. The use of MST to identify the binding affinity of junction binding agents is, to our knowledge, first reported example of this technique. The combined use of PAGE and MST provides complementary results for the visualisation of 3WJ and HJ formation and the direct binding affinity (Kd and EC50) of these agents. These assays can be used to aid the discovery and design of new therapeutics targeting non-canonical nucleic acid structures.

Metallohelices stabilize DNA three-way junctions and induce DNA damage in cancer cells

DNA three-way junctions (3WJ) represent one of the simplest supramolecular DNA structures arising as intermediates in homologous recombination in the absence of replication. They are also formed transiently during DNA replication. Here we examine the ability of Fe(II)-based metallohelices to act as DNA 3WJ binders and induce DNA damage in cells. We investigated the interaction of eight pairs of enantiomerically pure Fe(II) metallohelices with four different DNA junctions using biophysical and molecular biology methods. The results show that the metallohelices stabilize all types of tested DNA junctions, with the highest selectivity for the Y-shaped 3WJ and minimal selectivity for the 4WJ. The potential of the best stabilizer of DNA junctions and, at the same time, the most selective 3WJ binder investigated in this work to induce DNA damage was determined in human colon cancer HCT116 cells. These metallohelices proved to be efficient in killing cancer cells and triggering DNA damage that could yield therapeutic benefits.

Organometallic Pillarplexes That Bind DNA 4-Way Holliday Junctions and Forks

Holliday 4-way junctions are key to important biological DNA processes (insertion, recombination, and repair) and are dynamic structures that adopt either open or closed conformations, the open conformation being the biologically active form. Tetracationic metallo-supramolecular pillarplexes display aryl faces about a cylindrical core, an ideal structure to interact with open DNA junction cavities. Combining experimental studies and MD simulations, we show that an Au pillarplex can bind DNA 4-way (Holliday) junctions in their open form, a binding mode not accessed by synthetic agents before. Pillarplexes can bind 3-way junctions too, but their large size leads them to open up and expand that junction, disrupting the base pairing, which manifests in an increased hydrodynamic size and lower junction thermal stability. At high loading, they rearrange both 4-way and 3-way junctions into Y-shaped forks to increase the available junction-like binding sites. Isostructural Ag pillarplexes show similar DNA junction binding behavior but lower solution stability. This pillarplex binding contrasts with (but complements) that of metallo-supramolecular cylinders, which prefer 3-way junctions and can rearrange 4-way junctions into 3-way junction structures. The pillarplexes' ability to bind open 4-way junctions creates exciting possibilities to modulate and switch such structures in biology, as well as in synthetic nucleic acid nanostructures. In human cells, the pillarplexes do reach the nucleus, with antiproliferative activity at levels similar to those of cisplatin. The findings provide a new roadmap for targeting higher-order junction structures using a metallo-supramolecular approach, as well as expanding the toolbox available to design bioactive junction binders into organometallic chemistry.

Interactions of small molecules with DNA junctions

The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.

Characterization and Bioactivity of Polysaccharides Separated through a (Sequential) Biorefinery Process from Fucus spiralis Brown Macroalgae

Marine macroalgae biomass is a valuable renewable resource that can be used for the development of bioeconomy through the valorisation of valuable compounds. The aim of the current study is separate macroalgal polysaccharides with bioactive properties from brown macroalgae Fucus spiralis based on a designed biocascading biorefinery approach. Thus, we applied an integrated processing method for the separation of fucoidan and alginate, in addition to characterization through IR spectroscopy and ¹H NMR. The bioactivity potential (antioxidant activity using superoxide anion and DPPH radical scavenging analysis) of the two polysaccharides was evaluated, together with DNA binding studies performed though voltametric techniques and electronic spectroscopy titration. In terms of results, functional groups S=O (1226 cm⁻¹), N=S=O (1136 cm⁻¹) and C-O-SO₃ (1024 cm⁻¹), which are characteristic of fucoidan, were identified in the first polysaccharidic extract, whereas guluronic units (G) (1017 cm⁻¹) and mannuronic units (M) (872 and 812 cm⁻¹) confirmed the separation of alginate. The DNA binding studies of the isolated polysaccharides revealed an electrostatic and an intercalation interaction of DNA with fucoidan and alginate, respectively. Both antioxidant activity assays revealed improved antioxidant activity for both fucoidan and alginate compared to the standard α-tocopherol.

Measurement of the specific and non-specific binding energies of Mg2+ to RNA

Determining the non-specific and specific electrostatic contributions of magnesium binding to RNA is a challenging problem. We introduce a single-molecule method based on measuring the folding energy of a native RNA in magnesium and at its equivalent sodium concentration. The latter is defined so that the folding energy in sodium equals the non-specific electrostatic contribution in magnesium. The sodium equivalent can be estimated according to the empirical 100/1 rule (1 M NaCl is equivalent to 10 mM MgCl2), which is a good approximation for most RNAs. The method is applied to an RNA three-way junction (3WJ) that contains specific Mg2+ binding sites and misfolds into a double hairpin structure without binding sites. We mechanically pull the RNA with optical tweezers and use fluctuation theorems to determine the folding energies of the native and misfolded structures in magnesium (10 mM MgCl2) and at the equivalent sodium condition (1 M NaCl). While the free energies of the misfolded structure are equal in magnesium and sodium, they are not for the native structure, the difference being due to the specific binding energy of magnesium to the 3WJ, which equals ΔG≃ 10 kcal/mol. Besides stabilizing the 3WJ, Mg2+ also kinetically rescues it from the misfolded structure over timescales of tens of seconds in a force-dependent manner. The method should generally be applicable to determine the specific binding energies of divalent cations to other tertiary RNAs.

Selective recognition of A/T-rich DNA 3-way junctions with a three-fold symmetric tripeptide

Non-canonical DNA structures, particularly 3-Way Junctions (3WJs) that are transiently formed during DNA replication, have recently emerged as promising chemotherapeutic targets. Here, we describe a new approach to target 3WJs that relies on the cooperative and sequence-selective recognition of A/T-rich duplex DNA branches by three AT-Hook peptides attached to a three-fold symmetric and fluorogenic 1,3,5-tristyrylbenzene core.

Metallointercalators-DNA Tetrahedron Supramolecular Self-Assemblies with Increased Serum Stability

Self-assembly of metallointercalators into DNA nanocages is a rapid and facile approach to synthesize discrete bioinorganic host/guest structures with a high load of metal complexes. Turberfield's DNA tetrahedron can accommodate one intercalator for every two base pairs, which corresponds to 48 metallointercalators per DNA tetrahedron. The affinity of the metallointercalator for the DNA tetrahedron is a function of both the structure of the intercalating ligand and the overall charge of the complex, with a trend in affinity [Ru(bpy)₂(dppz)]²⁺ > [Tb-DOTAm-Phen]³⁺ ≫ Tb-DOTA-Phen. Intercalation of the metal complex stabilizes the DNA tetrahedron, resulting in an increase of its melting temperature and, importantly, a significant increase in its stability in the presence of serum. [Ru(bpy)₂(dppz)]²⁺, which has a greater affinity for DNA than [Tb-DOTAm-Phen]³⁺, increases the melting point and decreases degradation in serum to a greater extent than the Tb^III complex. In the presence of Lipofectamine, the metallointercalator@DNA nanocage assemblies substantially increase the cell uptake of their respective metal complex. Altogether, the facile incorporation of a large number of metal complexes per assembly, the higher stability in serum, and the increased cell penetration of metallointercalator@DNA make these self-assemblies well-suited as metallodrugs.

Oxidative DNA cleavage mediated by a new unexpected [Pd(BAPP)][PdCl4] complex (BAPP = 1,4-bis(3-aminopropyl)piperazine): crystal structure, DNA binding and cytotoxic behavior

A novel Pd(ii) double complex, [Pd(BAPP)][PdCl₄], containing the 1,4-bis(3-aminopropyl)piperazine (BAPP) ligand is investigated. X-ray crystallography of a single crystal confirmed the structure of the [Pd(BAPP)][PdCl₄] complex. The spectroscopic behavior was also elucidated using elemental analysis, nuclear magnetic resonance and Fourier-transform infrared spectroscopy, and mass spectrometry. The antimicrobial susceptibility of the [Pd(BAPP)][PdCl₄] complex against all tested microbial strains was lower than that of the BAPP ligand except for C. albicans. The cytotoxic impacts of the BAPP ligand and its [Pd(BAPP)][PdCl₄] complex were evaluated in vitro for HepG2, CaCo-2 and MCF7 cell lines as well as the WI-38 normal cell line. The anticancer activity was markedly improved by the complexation. The [Pd(BAPP)][PdCl₄] complex could selectively inhibit the tested cancer cells in a safe way to the non-tumorigenic cell (WI-38). From the DNA binding studies with ultraviolet-visible spectrophotometry, the [Pd(BAPP)][PdCl₄] complex interacts more efficiently with the calf thymus DNA than its BAPP ligand through the intercalative binding mode. In the absence of an external reductant, the [Pd(BAPP)][PdCl₄] complex cleaved the intact supercoiled pBR322 DNA under physiological conditions in a concentration-dependent manner. Additionally, electrophoretic experiments were performed in the presence of different radical scavengers, namely DMSO, NaN₃ and KI, and ruled out the hydrolytic mechanistic pathway of the reaction and suggested that the oxidative mechanism is the preferred one. The results of the binding affinity of the [Pd(BAPP)][PdCl₄] complex to human DNA were modeled using a molecular docking study showing that the complex interacts more strongly with human DNA than the ligand. Finally, an in vitro pharmacokinetic study was assessed through in silico ADME predictions.

Dinuclear nickel(ii) supramolecular helicates down-regulate gene expression in human cells by stabilizing DNA G-quadruplexes formed in the promoter regions

Dinuclear nickel(ii) supramolecular helicates selectively stabilize DNA G-quadruplexes and suppress G-quadruplex-regulated genes.

Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting

DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, U_bpy -3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand Ni^II (bpy)₃ complex at the junction core (ΔT_m =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside U_bpy -2, the degree of the Ni^II -mediated stabilization observed with U_bpy -3 was comparable to that of U_bpy -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of Ni^II ions. Furthermore, Ni^II -mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of Ni^II (bpy)₃ complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.

Click and Cut: a click chemistry approach to developing oxidative DNA damaging agents

Metallodrugs provide important first-line treatment against various forms of human cancer. To overcome chemotherapeutic resistance and widen treatment possibilities, new agents with improved or alternative modes of action are highly sought after. Here, we present a click chemistry strategy for developing DNA damaging metallodrugs. The approach involves the development of a series of polyamine ligands where three primary, secondary or tertiary alkyne-amines were selected and ‘clicked’ using the copper-catalysed azide-alkyne cycloaddition reaction to a 1,3,5-azide mesitylene core to produce a family of compounds we call the ‘Tri-Click’ (TC) series. From the isolated library, one dominant ligand (TC1) emerged as a high-affinity copper(II) binding agent with potent DNA recognition and damaging properties. Using a range of in vitro biophysical and molecular techniques—including free radical scavengers, spin trapping antioxidants and base excision repair (BER) enzymes—the oxidative DNA damaging mechanism of copper-bound TC1 was elucidated. This activity was then compared to intracellular results obtained from peripheral blood mononuclear cells exposed to Cu(II)–TC1 where use of BER enzymes and fluorescently modified dNTPs enabled the characterisation and quantification of genomic DNA lesions produced by the complex. The approach can serve as a new avenue for the design of DNA damaging agents with unique activity profiles.

Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells

DNA is intrinsically dynamic and folds transiently into alternative higher-order structures such as G-quadruplexes (G4s) and three-way DNA junctions (TWJs). G4s and TWJs can be stabilised by small molecules (ligands) that have high chemotherapeutic potential, either as standalone DNA damaging agents or combined in synthetic lethality strategies. While previous approaches have claimed to use ligands that specifically target either G4s or TWJs, we report here on a new approach in which ligands targeting both TWJs and G4s in vitro demonstrate cellular effects distinct from that of G4 ligands, and attributable to TWJ targeting. The DNA binding modes of these new, dual TWJ-/G4-ligands were studied by a panel of in vitro methods and theoretical simulations, and their cellular properties by extensive cell-based assays. We show here that cytotoxic activity of TWJ-/G4-ligands is mitigated by the DNA damage response (DDR) and DNA topoisomerase 2 (TOP2), making them different from typical G4-ligands, and implying a pivotal role of TWJs in cells. We designed and used a clickable ligand, TrisNP-α, to provide unique insights into the TWJ landscape in cells and its modulation upon co-treatments. This wealth of data was exploited to design an efficient synthetic lethality strategy combining dual ligands with clinically relevant DDR inhibitors.

Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication

The untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with molecular dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5' UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel anti-viral agents.

Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication*

The untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with molecular dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5' UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel anti-viral agents.

Metal-Coordinated Supramolecular Self-Assemblies for Cancer Theranostics

Metal-coordinated supramolecular nanoassemblies have recently attracted extensive attention as materials for cancer theranostics. Owing to their unique physicochemical properties, metal-coordinated supramolecular self-assemblies can bridge the boundary between traditional inorganic and organic materials. By tailoring the structural components of the metal ions and binding ligands, numerous multifunctional theranostic nanomedicines can be constructed. Metal-coordinated supramolecular nanoassemblies can modulate the tumor microenvironment (TME), thus facilitating the development of TME-responsive nanomedicines. More importantly, TME-responsive organic-inorganic hybrid nanomaterials can be constructed in vivo by exploiting the metal-coordinated self-assembly of a variety of functional ligands, which is a promising strategy for enhancing the tumor accumulation of theranostic molecules. In this review, recent advancements in the design and fabrication of metal-coordinated supramolecular nanomedicines for cancer theranostics are highlighted. These supramolecular compounds are classified according to the order in which the coordinated metal ions appear in the periodic table. Furthermore, the prospects and challenges of metal-coordinated supramolecular self-assemblies for both technical advances and clinical translation are discussed. In particular, the superiority of TME-responsive nanomedicines for in vivo coordinated self-assembly is elaborated, with an emphasis on strategies that enhance the accumulation of functional components in tumors for an ideal theranostic outcome.

Stereoselective Self-Assembly of DNA Binding Helicates Directed by the Viral β-Annulus Trimeric Peptide Motif

Combining coordination chemistry and peptide engineering offers extraordinary opportunities for developing novel molecular (supra)structures. Here, we demonstrate that the β-annulus motif is capable of directing the stereoselective assembly of designed peptides containing 2,2′-bipyridine ligands into parallel three-stranded chiral peptide helicates, and that these helicates selectively bind with high affinity to three-way DNA junctions.

Homo- and hetero-dinuclear Pt(II)/Pd(II) complexes: studies of hydrolysis, nucleophilic substitution reactions, DNA/BSA interactions, DFT calculations, molecular docking and cytotoxic activity

Three dinuclear complexes [Pd2(tpbd)Cl2]Cl2 (PP1), [Pt2(tpbd)Cl2]Cl2 (PP2) and [PdPt(tpbd)Cl2]Cl2 (PP3) (tpbd = N,N,N',N'-tetrakis(2-pyridylmethyl)benzene-1,4-diamine) have been synthesized and characterized and the protonation constants of their corresponding diaqua analogues have been determined. Also, in water solution, the aqua analogues of these complexes exist as mono-hydroxo, di-hydroxo and dimer μ-hydroxo complexes in the pH between 3.0 and 11.0. Substitution reactions with sulfur- and nitrogen-donor nucleophiles, such as thiourea (Tu), l-methionine (l-Met), glutathione (GSH) and guanosine-5'-monophosphate (5'-GMP), were studied at pH 7.2 by conventional and stopped-flow UV-Vis spectrophotometry and the observed reactivity follows the order: Tu > l-Met > GSH > 5'-GMP. Also, the interactions with calf thymus DNA (CT-DNA) and bovine serum albumin (BSA) were investigated. Competitive studies with DNA were performed in the presence of ethidium bromide and Hoechst dye 33258 as well. The complexes possess the strong ability to react with CT-DNA exhibiting intercalation and more preferable minor groove binding. Nevertheless, all complexes showed a good binding affinity toward BSA with relatively high binding constants. The nature of the binding forces between complexes and biomolecules has been identified as hydrophobic. Experimental results were compared with the molecular docking results, while the relative stability and thermodynamic properties of dinuclear complexes were compared with their mononuclear units by DFT calculations. Among three tested complexes, PP2 showed the most powerful cytotoxic effect on HTB140 and H460 cancer cell lines after 48 h of treatment and exerted a strong long-term influence on the proliferation potential of both tested cell lines. PP2 induced the inhibition of autophagy, G2/M cell cycle arrest and mitotic catastrophe.

Cavity-Containing [Fe2L3]4+ Helicates: An Examination of Host-Guest Chemistry and Cytotoxicity

Two new di(2,2′-bipyridine) ligands, 2,6-bis([2,2′-bipyridin]-5-ylethynyl)pyridine (L1) and bis(4-([2,2′-bipyridin]-5-ylethynyl)phenyl)methane (L2) were synthesized and used to generate two metallosupramolecular [Fe₂(L)₃](BF₄)₄ cylinders. The ligands and cylinders were characterized using elemental analysis, electrospray ionization mass spectrometry, UV-vis, ¹H-, ¹³C and DOSY nuclear magnetic resonance (NMR) spectroscopies. The molecular structures of the [Fe₂(L)₃](BF₄)₄ cylinders were confirmed using X-ray crystallography. Both the [Fe₂(L1)₃](BF₄)₄ and [Fe₂(L2)₃](BF₄)₄ complexes crystallized as racemic (rac) mixtures of the ΔΔ (P) and ΛΛ (M) helicates. However, ¹H NMR spectra showed that in solution the larger [Fe₂(L2)₃](BF₄)₄ was a mixture of the rac-ΔΔ/ΛΛ and meso-ΔΛ isomers. The host-guest chemistry of the helicates, which both feature a central cavity, was examined with several small drug molecules. However, none of the potential guests were found to bind within the helicates. In vitro cytotoxicity assays demonstrated that both helicates were active against four cancer cell lines. The smaller [Fe₂(L1)₃](BF₄)₄ system displayed low μM activity against the HCT116 (IC₅₀ = 7.1 ± 0.5 μM) and NCI-H460 (IC₅₀ = 4.9 ± 0.4 μM) cancer cells. While the antiproliferative effects against all the cell lines examined were less than the well-known anticancer drug cisplatin, their modes of action would be expected to be very different.

Recent advances in heteroleptic multiple-stranded metallosupramolecules

Well-ordered combination of defined coordination spheres and multiple types of ligands (heteroleptic) in a given structure can expand the structural complexity and functional diversity of the resulting metallosupramolecules. Such heteroleptic metallosupramolecular architectures are expected to afford advanced utility in a variety of applications. In this concise review article, recent advances in the development of multi-nuclear-cluster-based heteroleptic multiple-stranded (HLMS) metallosupramolecules are summarized and demonstrated. To construct HLMS metallosupramolecules, one type of multitopic ligands can be employed for building up multiple strands, while another type of ligands can be utilized to construct multi-nuclear clusters. Most HLMS metallosupramolecules adopt helical geometries and have high molecular symmetry, which can be key factors for the structural completion. HLMS metallosupramolecules can be used as basic building blocks for the fabrication of higher-order polymeric or discrete assembly architectures with well-defined geometries.

A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation

The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) AuI -CNC pincer complex suitable for oxidation to the redox-stable [AuIII (CNC)Cl]+ cation. Although the ligand salt and the [AuIII (CNC)Cl]+ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the AuIII complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [AuIII (CNC)Cl]+ complex behaves as a partial DNA intercalator. In silico screening indicated that the [AuIII (CNC)Cl]+ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the AuIII ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.

Rollover Cyclometalation vs Nitrogen Coordination in Tetrapyridyl Anticancer Gold(III) Complexes: Effect on Protein Interaction and Toxicity

In this work, a pair of gold(III) complexes derived from the analogous tetrapyridyl ligands H₂biqbpy1 and H₂biqbpy2 was prepared: the rollover, bis-cyclometalated [Au(biqbpy1)Cl ([1]Cl) and its isomer [Au(biqbpy2)Cl ([2]Cl). In [1]⁺, two pyridyl rings coordinate to the metal via a Au-C bond (C^∧N^∧N^∧C coordination) and the two noncoordinated amine bridges of the ligand remain protonated, while in [2]⁺ all four pyridyl rings of the ligand coordinate to the metal via a Au-N bond (N^∧N^∧N^∧N coordination), but both amine bridges are deprotonated. As a result, both complexes are monocationic, which allowed comparison of the sole effect of cyclometalation on the chemistry, protein interaction, and anticancer properties of the gold(III) compounds. Due to their identical monocationic charge and similar molecular shape, both complexes [1]Cl and [2]Cl displaced reference radioligand [³H]dofetilide equally well from cell membranes expressing the K_v11.1 (hERG) potassium channel, and more so than the tetrapyridyl ligands H₂biqbpy1 and H₂biqbpy2. By contrast, cyclometalation rendered [1]Cl coordinatively stable in the presence of biological thiols, while [2]Cl was reduced by a millimolar concentration of glutathione into metastable Au(I) species releasing the free ligand H₂biqbpy2 and TrxR-inhibiting Au⁺ ions. The redox stability of [1]Cl dramatically decreased its thioredoxin reductase (TrxR) inhibition properties, compared to [2]Cl. On the other hand, unlike [2]Cl, [1]Cl aggregated into nanoparticles in FCS-containing medium, which resulted in much more efficient gold cellular uptake. [1]Cl had much more selective anticancer properties than [2]Cl and cisplatin, as it was almost 10 times more cytotoxic to human cancer cells (A549, A431, A375, and MCF7) than to noncancerous cells (MRC5). Mechanistic studies highlight the strikingly different mode of action of the two compounds: while for [1]Cl high gold cellular uptake, nuclear DNA damage, and interaction with hERG may contribute to cell killing, for [2]Cl extracellular reduction released TrxR-inhibiting Au⁺ ions that were taken up in minute amounts in the cytosol, and a toxic tetrapyridyl ligand also capable of binding to hERG. These results demonstrate that bis-cyclometalation is an appealing method to improve the redox stability of Au(III) compounds and to develop gold-based cytotoxic compounds that do not rely on TrxR inhibition to kill cancer cells.

Targeting structural features of viral genomes with a nano-sized supramolecular drug

RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.

Supramolecular Coordination Complexes as Optical Biosensors

In recent years, luminescent supramolecular coordination complexes (SCCs), including 2D-metallacycles and 3D-metallacages have been utilised for biomolecular analysis. Unlike small-molecular probes, the dimensions, size, shape, and flexibility of these complexes can easily be tuned by combining ligands designed with particular geometries, symmetries and denticity with metal ions with strong geometrical binding preferences. The well-defined cavities that result, in combination with the other non-covalent interactions that can be programmed into the ligand design, facilitate great selectivity towards guest binding. In this Review we will discuss the application of luminescent metallacycles and cages in the binding and detection of a wide range of biomolecules, such as carbohydrates, proteins, amino acids, and biogenic amines. We aim to explore the effect of the structural diversity of SCCs on the extent of biomolecular sensing, expressed in terms of sensitivity, selectivity and detection range.

DNA folds threaten genetic stability and can be leveraged for chemotherapy

Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.

Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*

Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as Fe^II and Co^II . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled Fe^II helicate was internalized and selectively stains DNA replication factories in functional cells.

Metallohelices emulate the properties of short cationic α-helical peptides

Naturally occurring peptides in many living systems perform antimicrobial and anticancer host defence roles, but their potential for clinical application is limited by low metabolic stability and relatively high costs of goods. Self-assembled helical metal complexes provide an attractive synthetic platform for non-peptidic architectures that can emulate some of the properties of short cationic α-helical peptides, with tuneable charge, shape, size and amphipathicity. Correspondingly there is a growing body of evidence demonstrating that these supramolecular architectures exhibit bioactivity that emulates that of the natural systems. We review that evidence in the context of synthetic advances in the area, driven by the potential for biomedical applications. We note some design considerations for new biologically-relevant metallohelices, and give our outlook on the future of these compounds as therapeutic peptidomimetics.

Potent oxidation of DNA by Ru(ii) tri(polypyridyl) complexes under visible light irradiation via a singlet oxygen-mediated mechanism

The irradiation of Ru(ii) tri(polypridyl) complexes with visible light can induce potent oxidation of DNA mediated by ¹O₂via a type II photosensitization mechanism.

Design and Applications of Water-Soluble Coordination Cages

Compartmentalization of the aqueous space within a cell is necessary for life. In similar fashion to the nanometer-scale compartments in living systems, synthetic water-soluble coordination cages (WSCCs) can isolate guest molecules and host chemical transformations. Such cages thus show promise in biological, medical, environmental, and industrial domains. This review highlights examples of three-dimensional synthetic WSCCs, offering perspectives so as to enhance their design and applications. Strategies are presented that address key challenges for the preparation of coordination cages that are soluble and stable in water. The peculiarities of guest binding in aqueous media are examined, highlighting amplified binding in water, changing guest properties, and the recognition of specific molecular targets. The properties of WSCC hosts associated with biomedical applications, and their use as vessels to carry out chemical reactions in water, are also presented. These examples sketch a blueprint for the preparation of new metal-organic containers for use in aqueous solution, as well as guidelines for the engineering of new applications in water.

Coexistence of two quadruplex-duplex hybrids in the PIM1 gene

The triple-negative breast cancer (TNBC), a subtype of breast cancer which lacks of targeted therapies, exhibits a poor prognosis. It was shown recently that the PIM1 oncogene is highly related to the proliferation of TNBC cells. A quadruplex-duplex hybrid (QDH) forming sequence was recently found to exist near the transcription start site of PIM1. This structure could be an attractive target for regulation of the PIM1 gene expression and thus the treatment of TNBC. Here, we present the solution structures of two QDHs that could coexist in the human PIM1 gene. Form 1 is a three-G-tetrad-layered (3+1) G-quadruplex containing a propeller loop, a lateral loop and a stem-loop made up of three G•C Watson-Crick base pairs. On the other hand, Form 2 is an anti-parallel G-quadruplex comprising two G-tetrads and a G•C•G•C tetrad; the structure has three lateral loops with the middle stem-loop made up of two Watson-Crick G•C base pairs. These structures provide valuable information for the design of G-quadruplex-specific ligands for PIM1 transcription regulation.

Lighting up metallohelices: from DNA binders to chemotherapy and photodynamic therapy

The design of novel agents that specifically target DNA and interrupt its normal biological processes is an attractive goal in drug design. Among the promising metallodrugs, metal-directed self-assembled metallohelices with defined three-dimensional stereochemical structures display unique structure-inherent and unprecedented noncovalent targeting abilities towards DNA, resulting in excellent anticancer or antibiotic activities. A newly burgeoning hotspot is focusing on lighting them up by embedding luminescent metal ions as the vertices. The photoactive metallohelices that combine strong interactions toward DNA targets and efficient ¹O₂ quantum yield may provide new motivation in diagnostic and photodynamic therapy (PDT) areas. This perspective focuses on research progress on metallohelices as DNA binders and chemotherapeutic agents, and highlights recent advances in fabricating luminescent examples for PDT. The relative assembly strategies are also discussed and compared. Finally, perspectives on the future development of the lit-up metallohelices are presented.

Supramolecular DNA Three-Way Junction Motifs With a Bridging Metal Center

Various nano-sized supramolecular architectures have been constructed from DNA molecules via sequence-dependent self-assembly. A DNA three-way junction (3WJ), consisting of three oligonucleotides that are partially complementary to each other, is one of the simplest DNA supramolecular structures. This minireview covers studies on DNA 3WJ motifs bridged by an interstrand metal complex with some related works. The incorporation of interstrand metal complexes into DNA has attracted increasing attention because it potentially allows for metal-dependent regulation of the thermal stability and the structure of DNA supramolecules. Metal-bridged DNA 3WJs were synthesized from three DNA strands containing a bipyridine (bpy)-modified nucleotide in the presence of appropriate metal ions. The bpy-modified DNA strands were crosslinked by an interstrand 3:1 metal complex [Ni^II(bpy)₃ etc.] at the junction core. As a result, the thermal stability of the 3WJs was significantly enhanced upon metal complexation. Furthermore, metal-mediated structural transformation between DNA duplexes and 3WJs was demonstrated by using the same bpy-modified DNA strands. A mixture of bpy-modified strands and their natural complementary strands were self-assembled exclusively into duplexes in the absence of any transition metal ions. In contrast, addition of Ni^II ions induced the formation of 3WJs through the formation of an interstrand Ni^II(bpy)₃ complex, which served as a template for the 3WJ assembly. Because DNA 3WJ structures are essential structural motifs for DNA-based nanoarchitectures, the metal-mediated stabilization and structural induction of metal-locked 3WJs would lead to many potential applications to artificial DNA architectures.

Synthesis and anti-proliferative activities of amine capped Pd and Pt macrocycles of 4,4′-dipyridylselenides

Symmetric macrocyclic complexes characterized as dimeric and their oligomeric form in water and the solid state exhibit high in vitro anticancer activities.

DNA Junction Ligands Trigger DNA Damage and Are Synthetic Lethal with DNA Repair Inhibitors in Cancer Cells

Translocation of DNA and RNA polymerases along their duplex substrates results in DNA supercoiling. This torsional stress promotes the formation of plectonemic structures, including three-way DNA junction (TWJ), which can block DNA transactions and lead to DNA damage. While cells have evolved multiple mechanisms to prevent the accumulation of such structures, stabilizing TWJ through ad hoc ligands offer an opportunity to trigger DNA damage in cells with high levels of transcription and replication, such as cancer cells. Here, we develop a series of azacryptand-based TWJ ligands, we thoroughly characterize their TWJ-interacting properties in vitro and demonstrate their capacity to trigger DNA damage in rapidly dividing human cancer cells. We also demonstrate that TWJ ligands are amenable to chemically induced synthetic lethality strategies upon association with inhibitors of DNA repair, thus paving the way toward innovative drug combinations to fight cancers.