Crystal structure of Δ-[Ru(bpy)₂dppz]²⁺ bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation

Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ-[Ru(phen)2 phi]2

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ-[Ru(phen)2 phi]2+ , where phi=9,10-phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2 . The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ-enantiomer and show a high affinity for TA/TA steps and, more generally, TA-rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence.

Investigating the Cytotoxicity of Ru(II) Polypyridyl Complexes by Changing the Electronic Structure of Salicylaldehyde Ligands

A novel class of Ru(II)-based polypyridyl complexes with an auxiliary salicylaldehyde ligand [Ru(phen)2(X-Sal)]BF4 {X: H (1), 5-Cl (2), 5-Br (3), 3,5-Cl2 (4), 3,5-Br2 (5), 3-Br,5-Cl (6), 3,5-I2 (7), 5-NO2 (8), 5-Me (9), 4-Me (10), 4-OMe (11), and 4-DEA (12), has been synthesized and characterized by elemental analysis, FT-IR, and 1H/13C NMR spectroscopy. The molecular structure of 4, 6, 9, 10, and 11 was determined by single-crystal X-ray diffraction analysis which revealed structural similarities. DFT and TD-DFT calculations showed that they also possess similar electronic structures. Absorption/emission spectra were recorded for 2, 3, 10, and 11. All Ru-complexes, unlike the pure ligands and the complex lacking the salicylaldehyde component, displayed outstanding antiproliferative activity in the screening test (10 μM) against CCRF-CEM leukemia cells underlining the crucial role of the presence of the auxiliary ligand for the biological activity. The two most active derivatives, namely 7 and 10, were selected for continuous assays showing IC50 values in the submicromolar and micromolar range against drug-sensitive CCRF-CEM and multidrug-resistant CEM/ADR5000 leukemia cells, respectively. These two compounds were investigated in silico for their potential binding to duplex DNA well-matched and mismatched base pairs, since they showed remarkable selectivity indexes (2.2 and 19.5 respectively) on PBMC cells.

New Tridentate Ligand Affords a Long-Lived 3MLCT Excited State in a Ru(II) Complex: DNA Photocleavage and 1O2 Production

Two new complexes, [Ru(tpy)(qdppz)](PF6)2 (1; qdppz = 2-(quinolin-8-yl)dipyrido[3,2-a:2',3'-c]phenazine, tpy = 2,2':6',2″-terpyridine) and [Ru(qdppz)2](PF6)2 (2), were investigated for their potential use as phototherapeutic agents through their ability to photosensitize the production of singlet oxygen, 1O2, upon irradiation with visible light. The complexes exhibit strong Ru(dπ) → qdppz(π*) metal-to-ligand charge transfer (MLCT) absorption with maxima at 485 and 495 nm for 1 and 2 in acetone, respectively, red-shifted from the Ru(dπ) → tpy(π*) absorption at 470 nm observed for [Ru(tpy)2]2+ (3) in the same solvent. Complexes 1 and 3 are not luminescent at room temperature, but 3MLCT emission is observed for 2 with maximum at 690 nm (λexc = 480 nm) in acetone. The lifetimes of the 3MLCT states of 1 and 2 were measured using transient absorption spectroscopy to be ∼9 and 310 ns in methanol, respectively, at room temperature (λexc = 490 nm). The bite angle of the qdppz ligand is closer to octahedral geometry than that of tpy, resulting in the longer lifetime of 2 as compared to those of 1 and 3. Arrhenius treatment of the temperature dependence of the luminescence results in similar activation energies, Ea, from the 3MLCT to the 3LF (ligand-field) state for the two complexes, 2520 cm-1 in 1 and 2400 cm-1 in 2. However, the pre-exponential factors differ by approximately two orders of magnitude, 2.3 × 1013 s-1 for 1 and 1.4 × 1011 s-1 for 2, which, together with differences in the Huang-Rhys factors, lead to markedly different 3MLCT lifetimes. Although both 1 and 2 intercalate between the DNA bases, only 2 is able to photocleave DNA owing to its 1O2 production upon irradiation with ΦΔ = 0.69. The present work highlights the profound effect of the ligand bite angle on the electronic structure, providing guidelines for extending the lifetime of 3MLCT Ru(II) complexes with tridentate ligands, a desired property for a number of applications.

Anticancer properties of complexes derived from bidentate ligands

Cancer is the abnormal division and multiplication of cells in an organ or tissue. It is the second leading cause of death globally. There are various types of cancer such as prostate, breast, colon, lung, stomach, liver, skin, and many others depending on the tissue or organ where the abnormal growth originates. Despite the huge investment in the development of anticancer agents, the transition of research to medications that improve substantially the treatment of cancer is less than 10%. Cisplatin and its analogs are ubiquitous metal-based anticancer agents notable for the treatment of various cancerous cells and tumors but unfortunately accompanied by large toxicities due to low selectivity between cancerous and normal cells. The improved toxicity profile of cisplatin analogs bearing bidentate ligands has motivated the synthesis of vast metal complexes of bidentate ligands. Complexes derived from bidentate ligands such as β-diketones, diolefins, benzimidazoles and dithiocarbamates have been reported to possess 20 to 15,600-fold better anticancer activity, when tested on cell lines, than some known antitumor drugs currently on the market, e.g. cisplatin, oxaliplatin, carboplatin, doxorubicin, and 5-fluorouracil. This work discusses the anticancer properties of various metal complexes derived from bidentate ligands, for possible application in chemotherapy. The results discussed were evaluated by the IC50 values as obtained from cell line tests on various metal-bidentate complexes. The structure-activity relationship study of the complexes discussed, revealed that hydrophobicity is a key factor that influences anticancer properties of molecules.

Enabling programmable dynamic DNA chemistry using small-molecule DNA binders

The binding of small molecules to the double helical structure of DNA, through either intercalation or minor groove binding, may significantly alter the stability and functionality of DNA, which is a fundamental basis for many therapeutic and sensing applications. Here, we report that small-molecule DNA binders can also be used to program reaction pathways of a dynamic DNA reaction, where DNA strand displacement can be tuned quantitatively according to the affinity, charge, and concentrations of a given DNA binder. The binder-induced nucleic acid strand displacement (BIND) thus enables innovative technologies to accelerate the discovery and characterization of bioactive small molecules. Specifically, we demonstrate the comprehensive characterization of existing and newly discovered DNA binders, where critical parameters for binding affinity and sequence selectivity can be obtained in a single, unbiased molecular platform without the need for any specialized equipment. We also engineer a tandem BIND system as a high-throughput screening assay for discovering DNA binders, through which 8 DNA binders were successfully discovered from a library of 700 compounds.

Optically Pure Double-Stranded Dinuclear Ir(III) Metallohelices Enabled Chirality-Induced Photodynamic Responses

Investigation on the interactions between enantiomers of chiral drugs and biomolecules can help precisely understand their biological behaviors in vivo and provide insights into the design of new drugs. Herein, we designed and synthesized a pair of optically pure, cationic, double-stranded dinuclear Ir(III)-metallohelices (Λ₂R₄-H and Δ₂S₄-H), and their dramatic enantiomer-dependent photodynamic therapy (PDT) responses were thoroughly studied in vitro and in vivo. Compared to the mononuclear enantiomeric or racemic [Ir(ppy)₂(dppz)][PF₆] (Λ-/Δ-Ir, rac-Ir) that with high dark toxicity and low photocytotoxicity index (PI) values, both of the optically pure metallohelices displayed negligible toxicity in the dark while exhibiting very distinctive light toxicity upon light irradiation. The PI value of Λ₂R₄-H was approximately 428, however, Δ₂S₄-H significantly reached 63,966. Interestingly, only Δ₂S₄-H was found to migrate from mitochondria to nucleus after light irradiation. Further proteomic analysis verified that Δ₂S₄-H activated the ATP-dependent migration process after light irradiation, and subsequently inhibited the activities of the nuclear proteins such as superoxide dismutase 1 (SOD1) and eukaryotic translation initiation factor 5A (EIF5A) to trigger the accumulation of superoxide anions and downregulate mRNA splicing processes. Molecular docking simulations suggested that the interactions between metallohelices and nuclear pore complex NDC1 dominated the migration process. This work presents a new kind of Ir(III) metallohelices-based agent with the highest PDT efficacy, highlights the importance of metallohelices' chirality, and provides inspirations for the future design of chiral helical metallodrugs.

Piano-stool ruthenium(II) complexes with maleimide and phosphine or phosphite ligands: synthesis and activity against normal and cancer cells

In these studies, we designed and investigated cyto- and genotoxic potential of five ruthenium cyclopentadienyl complexes bearing different phosphine and phosphite ligands. All of the complexes were characterized with spectroscopic analysis (NMR, FT-IR, ESI-MS, UV-vis, fluorescence and XRD (for two compounds)). For biological studies, we used three types of cells - normal peripheral blood mononuclear (PBM) cells, leukemic HL-60 cells and doxorubicin-resistance HL-60 cells (HL-60/DR). We compared the results obtained with those obtained for the complex with maleimide ligand CpRu(CO)₂(η¹-N-maleimidato) 1, which we had previously reported. We observed that the complexes CpRu(CO)(PPh₃)(η¹-N-maleimidato) 2a and CpRu(CO)(P(OEt)₃)(η¹-N-maleimidato) 3a were the most cytotoxic for HL-60 cells and non-cytotoxic for normal PBM cells. However, complex 1 was more cytotoxic for HL-60 cells than complexes 2a and 3a (IC₅₀ = 6.39 μM vs. IC₅₀ = 21.48 μM and IC₅₀ = 12.25 μM, respectively). The complex CpRu(CO)(P(OPh)₃)(η¹-N-maleimidato) 3b is the most cytotoxic for HL-60/DR cells (IC₅₀ = 104.35 μM). We found the genotoxic potential of complexes 2a and 3a only in HL-60 cells. These complexes also induced apoptosis in HL-60 cells. Docking studies showed that complexes 2a and CpRu(CO)(P(Fu)₃)(η¹-N-maleimidato) 2b have a small ability to degrade DNA, but they may cause a defect in DNA damage repair mechanisms leading to cell death. This hypothesis is corroborated with the results obtained in the plasmid relaxation assay in which ruthenium complexes bearing phosphine and phosphite ligands induce DNA breaks.

Design, synthesis, biomedical investigation, DFT calculation and molecular docking of novel Ru(II)-mixed ligand complexes

A novel series of bioactive water-soluble mononuclear Ru(II)-mixed ligand complexes of 2,2'-bipyridyl and V-shaped Schiff base ligands were synthesized and structurally characterized. Biomedical activities of Ru(II) complexes have been tested in view of antioxidant activities, interaction with calf thymus DNA (CT-DNA), and anticancer performance. The optimized structure of these complexes has been further supported by density functional theory (DFT) calculations. Further, validation of the interaction studies of some complexes was accomplished by carrying out molecular docking studies with DNA using molecular operating environment (MOE) software are reported.Communicated by Ramaswamy H. Sarma.

Deconvoluting binding sites in amyloid nanofibrils using time-resolved spectroscopy

Steady-state fluorescence spectroscopy has a central role not only for sensing applications, but also in biophysics and imaging. Light switching probes, such as ruthenium dipyridophenazine complexes, have been used to study complex systems such as DNA, RNA, and amyloid fibrils. Nonetheless, steady-state spectroscopy is limited in the kind of information it can provide. In this paper, we use time-resolved spectroscopy for studying binding interactions between amyloid-β fibrillar structures and photoluminescent ligands. Using time-resolved spectroscopy, we demonstrate that ruthenium complexes with a pyrazino phenanthroline derivative can bind to two distinct binding sites on the surface of fibrillar amyloid-β, in contrast with previous studies using steady-state photoluminescence spectroscopy, which only identified one binding site for similar compounds. The second elusive binding site is revealed when deconvoluting the signals from the time-resolved decay traces, allowing the determination of dissociation constants of 3 and 2.2 μM. Molecular dynamic simulations agree with two binding sites on the surface of amyloid-β fibrils. Time-resolved spectroscopy was also used to monitor the aggregation of amyloid-β in real-time. In addition, we show that common polypyridine complexes can bind to amyloid-β also at two different binding sites. Information on how molecules bind to amyloid proteins is important to understand their toxicity and to design potential drugs that bind and quench their deleterious effects. The additional information contained in time-resolved spectroscopy provides a powerful tool not only for studying excited state dynamics but also for sensing and revealing important information about the system including hidden binding sites.

Ruthenium(II) Polypyridyl Complexes as FRET Donors: Structure- and Sequence-Selective DNA-Binding and Anticancer Properties

Ruthenium(II) polypyridyl complexes (RPCs) that emit from metal-to-ligand charge transfer (MLCT) states have been developed as DNA probes and are being examined as potential anticancer agents. Here, we report that MLCT-emissive RPCs that bind DNA undergo Förster resonance energy transfer (FRET) with Cy5.5-labeled DNA, forming mega-Stokes shift FRET pairs. Based on this discovery, we developed a simple and rapid FRET binding assay to examine DNA-binding interactions of RPCs with diverse photophysical properties, including non-"light switch" complexes [Ru(dppz)₂(5,5'dmb)]²⁺ and [Ru(PIP)₂(5,5'dmb)]²⁺ (dppz = dipyridophenazine, 5,5'dmb = 5,5'-dimethyl-2,2'-bipyridine, PIP = 2-phenyl-imidazo[4,5-f][1,10]phenanthroline). Binding affinities toward duplex, G-quadruplex, three-way junction, and mismatch DNA were determined, and derived FRET donor-acceptor proximities provide information on potential binding sites. Molecules characterized by this method demonstrate encouraging anticancer properties, including synergy with the PARP inhibitor Olaparib, and mechanistic studies indicate that [Ru(PIP)₂(5,5'dmb)]²⁺ acts to block DNA replication fork progression.

Antileukemia Activity and Mechanism of Platinum(II)-Based Metal Complexes

Transition metal complexes have continued to constitute an appealing class of medicinal compounds since the exceptional discovery of cisplatin in the late 1960s. Pt(II)-based complexes are endowed with a broad range of biological properties, which are mainly exerted by targeting DNA. In this study, we report a significant biological investigation into and computation analyses of four Pt(II)-complexes, namely, LDP-1-4, synthesized and characterized according to previously reported procedures. Molecular-modelling studies highlighted that the top two LDP compounds (i.e., LDP-1 and LDP-4) might bind to both matched and mismatched base pair sites of the oligonucleotide 5'-(dCGGAAATTACCG)₂-3', supporting their anticancer potential. These two complexes displayed noteworthy cytotoxicity in vitro (sub-micromolar-micromolar range) against two leukaemia cell lines, i.e., CCRF-CEM and its multi-drug-resistant counterpart CEM/ADR5000, and remarkable anti-angiogenic properties (in the sub-micromolar range) evaluated in an in vivo model, i.e., a chick embryo chorioallantoic membrane (CAM) assay.

Evaluation of 1 H-NMR Spectroscopy-Based Quantification Methods of the Supramolecular Aggregation of a Molecular Photosensitizer

The supramolecular dimerization of a ruthenium polypyridyl precursor of a well-developed family of hydrogen evolving photocatalysts via π-π-interactions of the polyheteroaromatic bridging ligand was quantified with concentration dependent ¹ H-NMR-spectroscopy. The data sets were analyzed with different calculation and fit methods. A comparison between the results of direct calculation, linear and nonlinear approaches showed that the application of a global nonlinear fit procedure yields the best results. The presented methods are also applicable for dimerization processes in solution of other molecular moieties.

Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone

The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH₂ groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH₂. The trends in the energy decomposition analysis for the interaction energy, ΔE_int, showed that the ΔE_elstat contributions are equal or even a little bit higher than the values for ΔE_disp. Such important ΔE_elstat attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH₂ functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔE_disp is the most important attractive contribution to the ΔE_int. The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.

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.

Anomalous Enhancement of Electrochemical Charge Transfer by a Ru Complex Ion Intercalator

We have found that the DNA intercalator [Ru(bpy)₂DPPZ]²⁺ (bpy = 2,2'-bipyridine; DPPZ = dipyrido[3,2-a:2',3'-c]phenazine) causes an anomalous increase in charge transfer in electrochemical impedance spectroscopy (EIS). With a carbonaceous electrode and a 1 mM hexacyanoferrate (1 mM [Fe(CN)₆]^3- and 1 mM [Fe(CN)₆]^4-) mediator, we found that adding only 1 μM [Ru(bpy)₂DPPZ]²⁺ greatly enhanced the charge transfer between the electrode and hexacyanoferrate mediator, independently of other electrolytes or buffer components. The effect started with a one millionth amount of hexacyanoferrate. Since [Ru(bpy)₂DPPZ]²⁺ can intercalate with dsDNA, the effect is highly applicable for dsDNA detection or PCR monitoring. With further developments of this method, EIS sensors not requiring specific electrode modifications should be possible.

Recent Strategies to Develop Innovative Photosensitizers for Enhanced Photodynamic Therapy

This review presents a robust strategy to design photosensitizers (PSs) for various species. Photodynamic therapy (PDT) is a photochemical-based treatment approach that involves the use of light combined with a light-activated chemical, referred to as a PS. Attractively, PDT is one of the alternatives to conventional cancer treatment due to its noninvasive nature, high cure rates, and low side effects. PSs play an important factor in photoinduced reactive oxygen species (ROS) generation. Although the concept of photosensitizer-based photodynamic therapy has been widely adopted for clinical trials and bioimaging, until now, to our surprise, there has been no relevant review article on rational designs of organic PSs for PDT. Furthermore, most of published review articles in PDT focused on nanomaterials and nanotechnology based on traditional PSs. Therefore, this review aimed at reporting recent strategies to develop innovative organic photosensitizers for enhanced photodynamic therapy, with each example described in detail instead of providing only a general overview, as is typically done in previous reviews of PDT, to provide intuitive, vivid, and specific insights to the readers.

Synthesis and DNA interaction studies of Ru(II) cell penetrating peptide (CPP) bioconjugates

The synthesis of the first bioconjugates of a set of ruthenium(II) dipyridophenazine complexes with two different cell penetrating peptides (CPPs) is described. The CPPs, an arginine rich TAT-9 (RKKRRQRRR) sequence and the Xentry peptide (LCLRPVG), were synthesized using standard SPPS protocols, and the bioconjugates were obtained by the microwave-assisted coupling of the HOBt/TBTU preactivated metal complexes with the respective peptides on Wang resin. The racemic metal complexes were obtained by modified literature procedures. The bioconjugates were cleaved from the resin, purified by semi-preparative HPLC and characterized by analytical HPLC, high resolution mass spectrometry (HR-MS), and NMR spectroscopy. Despite the bioconjugation of the peptides to the dppz ligand, DNA intercalation was observed by CD spectroscopy, viscometry and the characteristic switch-on fluorescence of this class of compounds. Furthermore, the cellular uptake of the Xentry bioconjugates was confirmed by live cell imaging. Like the parent metal complexes, the bioconjugates show low in vitro cytotoxicity (IC₅₀ > 80 μM), which is similar to the respective metal complexes alone.

Switching the Mechanism of NADH Photooxidation by Supramolecular Interactions

A series of three Ru(II) polypyridine complexes was investigated for the selective photocatalytic oxidation of NAD(P)H to NAD(P)⁺ in water. A combination of (time‐resolved) spectroscopic studies and photocatalysis experiments revealed that ligand design can be used to control the mechanism of the photooxidation: For prototypical Ru(II) complexes a ¹O₂ pathway was found. Rudppz ([(tbbpy)₂Ru(dppz)]Cl₂, tbbpy=4,4'‐di‐tert‐butyl‐2,2'‐bipyridine, dppz=dipyrido[3,2‐a:2′,3′‐c]phenazine), instead, initiated the cofactor oxidation by electron transfer from NAD(P)H enabled by supramolecular binding between substrate and catalyst. Expulsion of the photoproduct NAD(P)⁺ from the supramolecular binding site in Rudppz allowed very efficient turnover. Therefore, Rudppz permits repetitive selective assembly and oxidative conversion of reduced naturally occurring nicotinamides by recognizing the redox state of the cofactor under formation of H₂O₂ as additional product. This photocatalytic process can fuel discontinuous photobiocatalysis.

Crystalline ruthenium polypyridine nanoparticles: a targeted treatment of bacterial infection with multifunctional antibacterial, adhesion and surface-anchoring photosensitizer properties

Photodynamic antibacterial therapy employs nanocomposites as an alternative to traditional antibiotics for the treatment of bacterial infections. However, many of these antibacterial materials are less effective towards bacteria than traditional drugs, either due to poor specificity or antibacterial activity. This can result in needless and excessive drug use in treatments. This paper describes a multifunctional drug delivery nanoparticle (MDD-NP), Sph-Ru-MMT@PZ, based on the nanostructured-form of [Ru(bpy)2dppz] (PF6)2 (Sph-Ru), which has adhesive properties towards its microbial targets as well as surface-anchoring photosensitizer effects. The design and construction of MDD-NP is based on the adhesive properties of the outer layers of montmorillonite (MMT), which allows Sph-Ru-MMT@PZ to successfully reach its bacterial target; the outer layer of the E. coli. In addition, under 670 nm red irradiation therapy (R-IT), the surface-anchoring properties use the photosensitizer phthalocyanine zinc (PZ) to destroy the bacteria by producing reactive oxygen species (ROS) which causes cell lysis of E. coli. More importantly, Sph-Ru-MMT@PZ has no fluorescence response to live E. coli with intact cell membranes but selectively stained and demonstrated fluorescence during membrane damage of early-stage cells as well as exposure of nuclear materials at late-stage of cell lysis. Sph-Ru-MMT@PZ showed beneficial and synergistic anti-infective effects in vivo by inhibiting the E. coli infection-induced inflammatory response and eventually promoting wound healing in mice. This new strategy for high precision antibacterial therapy towards specific targets, provides an exciting opportunity for the application of multifunctional nanocomposites towards microbial infections.

New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes

This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.

A platform for on-the-complex annulation reactions with transient aryne intermediates

Organometallic complexes are ubiquitous in chemistry and biology. Whereas their preparation has historically relied on ligand synthesis followed by coordination to metal centers, the ability to efficiently diversify their structures remains a synthetic challenge. A promising yet underdeveloped strategy involves the direct manipulation of ligands that are already bound to a metal center, also known as chemistry-on-the-complex. Herein, we introduce a versatile platform for on-the-complex annulation reactions using transient aryne intermediates. In one variant, organometallic complexes undergo transition metal-catalyzed annulations with in situ generated arynes to form up to six new carbon-carbon bonds. In the other variant, an organometallic complex bearing a free aryne is generated and intercepted in cycloaddition reactions to access unique scaffolds. Our studies, centered around privileged polypyridyl metal complexes, provide an effective strategy to annulate organometallic complexes and access complex metal-ligand scaffolds, while furthering the synthetic utility of strained intermediates in chemical synthesis.

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.

Structural insights into the recognition of DNA defects by small molecules

Studies on the binding interaction of small molecules and nucleic acids have been explored for their biological applications. With excellent photophysical/chemical properties, numerous metal complexes have been studied as structural probes for nucleic acids. The recognition of DNA defects is of high importance due to their association with various types of cancers. Small molecules that target DNA defects in a specific and selective manner offer a new avenue for developing novel drugs and diagnostic tools. Transition metal complexes have been studied as probes for abasic sites and DNA/RNA mismatches. By changing the ligand structure or metal center, the probing efficiency of the metal complexes varies towards the defects. In this perspective, we have discussed mainly the structural requirement of metal complexes as probes for abasic sites, mismatches, and covalent DNA adducts, followed by the challenges and future directions.

Nanocatalytic Innate Immunity Activation by Mitochondrial DNA Oxidative Damage for Tumor-Specific Therapy

The innate immune system plays a key role in protecting the human body from tumors, which, unfortunately, is largely counteracted by their immune-suppression function. Such an immune suppression has been reported to be induced by the immunosuppressive microenvironment, including the exhausted cytotoxic T lymphocytes (CTLs) and tumor-promoting M2-polarized macrophages. Here, a novel tumor-immunotherapeutic modality based on the nanocatalytic innate immunity activation by tumor-specific mitochondrial DNA (mtDNA) oxidative damage is proposed. In detail, a nanocatalytic medicine, Fe²⁺ -Ru²⁺ -loaded mesoporous silica nanoparticle named as MSN-Ru²⁺ /Fe²⁺ (MRF), is constructed to induce oxidative damage in the mtDNA of tumor cells. Such an oxidative mtDNA is able to escape from the tumor cells and acts as an immunogenic damage-associated molecular pattern to M1-polarize tumor-associated macrophages (TAMs), resulting in the reactivated immunoresponse of macrophages against cancer cells, and the subsequent inflammatory response of innate immunity. Most importantly, the treatment strategy based on regulating the innate immune response of TAMs not only stops the primary tumor progression, but also almost completely inhibits the growth of distant tumors in the periods of treatments.

Bis(bipyridine)ruthenium(II) Ferrocenyl β-Diketonate Complexes: Exhibiting Nanomolar Potency against Human Cancer Cell Lines

The synthesis and characterization of new bis(bipyridine)ruthenium(II) ferrocenyl β-diketonate complexes, [(bpy)2 Ru(Fc-acac)][PF6 ] (bpy=2,2'-bipyridine; Fc-acac=functionalized ferrocenyl β-diketonate ligand) are reported. Alongside clinical platinum drugs, these bimetallic ruthenium-iron complexes have been screened for their cytotoxicity against MIA PaCa-2 (human pancreatic carcinoma), HCT116 p53+/+ (human colon carcinoma, p53-wild type) and ARPE-19 (human retinal pigment epithelial) cell lines. With the exception of one complex, the library exhibit nanomolar potency against cancerous cell lines, and their relative potencies are up to 40x, 400x and 72x more cytotoxic than cisplatin, carboplatin and oxaliplatin, respectively. Under hypoxic conditions, the complexes remain cytotoxic (sub-micromolar range), highlighting their potential in targeting hypoxic tumor regions. The Comet assay was used to determine their ability to damage DNA, and results show dose dependent damage which correlates well with the cytotoxicity results. Their potential to treat bacterial and fungal strains has been determined, and highlight complexes have selective growth inhibition of up to 87-100 % against Staphylococcus aureus and Candida albicans.

Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO

Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)_n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)₆. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π^* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.

Elucidating the intercalation of methylated 1,10-phenanthroline with DNA: the important weight of the CH/H interactions and the selectivity of CH/π and CH/n interactions

Flat molecules like phenanthroline derivatives intercalate between base pairs of deoxyribonucleic acid and produce cytotoxic effects against tumoral cells. Elucidating the way of intercalation and its modulation on their efficiency by substitution still remains a challenging topic of research. In this work we analysed the intercalation via the major groove of methylated derivatives of phenanthroline, in different number and position, between guanine-cytosine base pairs. We studied our systems by using semi-empirical methods and density functional theory including dispersion corrections with the PM6-DH2 Hamiltonian and the B3LYP-D3 functional. We explored the geometry and electronic structure by means of the quantum theory of atoms in molecules and non-covalent interactions index analyses, whereas the interaction energy was estimated by means of two different approaches: one taking into account the results from the quantum theory of atoms in molecules analysis and the other based on the so-called energy decomposition analysis. The effect of solvation was also taken into consideration. Our studies show that CH/π and CH/n interactions by means of the -CH3 groups of methylated phen follow a clear pattern for any number of -CH3 groups and their position in the methylated phen ligand. That is, they try to produce the CH/π and CH/n interactions with the O and N heteroatoms of the base pairs and with the O atoms of the sugar and phosphate backbone. These findings suggest that the modulation of the intercalation of ligands that are able to form CH/π and CH/n weak interactions with the deoxyribonucleic acid is ruled not only by the number and position of the substitutions of the ligands but also by some key sites, which are the O and N atoms of the deoxyribonucleic acid in our analysed systems. It suggests some key and lock mechanism in which the interacting fragments fit like puzzle pieces in order to achieve the optimal interaction for the stabilization of the system. Interaction energies were calculated by using different approaches which converged to similar trends about the number and position of the -CH3 groups. The important weight of the CH/H interactions in the total interaction energy must be highlighted.

Recognizing and stabilizing miR-21 by chiral ruthenium(II) complexes

MiR-21, a non-coding miRNA with 22 nucleotides, plays an important part in the proliferation, invasion, and metastasis of tumor cells. The present study demonstrates that isomers of chiral ruthenium(II) complexes with alkynes (Λ-1 and Δ-1) were synthesized by Songogashira coupling reaction by using microwave-assisted synthetic technology. The isomers can recognize and stabilize miR-21, with the Λ-isomer showing a stronger binding capacity than the Δ-isomer. Further studies showed that both isomers can be uptaken by MDA-MB-231 cells and enriched in the nucleus. Treatment with the Λ-/Δ-isomer downregulated the expression of miR-21. In a word, the development of chiral ruthenium(II) complexes act as potential inhibitors against tumor cells by recognizing, stabilizing, and regulating the expression of miR-21.

Comparative studies on the binding interaction of two chiral Ru(II) polypyridyl complexes with triple- and double-helical forms of RNA

Two chiral Ru(II) polypyridyl complexes, Δ-[Ru(bpy)₂(6-F-dppz)]²⁺ (Δ-1; bpy = 2,2'-bipyridine, 6-F-dppz = 6-fluorodipyrido[3,2-a:2',3'-c]phenazine) and Λ-[Ru(bpy)₂(6-F-dppz)]²⁺ (Λ-1), have been synthesized and characterized as binders for the RNA poly(U)•poly(A)*poly(U) triplex and poly(A)•poly(U) duplex in this work. Analysis of the UV-Vis absorption spectra and fluorescence emission spectra indicates that the binding of intercalating Δ-1 with the triplex and duplex RNA is greater than that of Λ-1, while the binding affinities of the two enantiomers to triplex structure is stronger than that of duplex structure. Fluorescence titrations show that the two enantiomers can act as molecular "light switches" for triple- and double-helical RNA. Thermal denaturation studies revealed that that the two enantiomers are more stable to Watson-Crick base-paired double strand of the triplex than the Hoogsteen base-paired third strand, but their stability and selectivity are different. For Δ-enantiomer, the increase of the thermal stability of the Watson-Crick base-paired duplex (13 °C) is slightly stronger than of the Hoogsteen base-paired strand (10 °C), displaying no obvious selectivity. However, compared to the Hoogsteen base-paired strand (5 °C), the stability of the Λ-enantiomer to the Watson-Crick base-paired duplex (13 °C) is more significant, which has obvious selectivity. The overall increase in viscosity of the RNA-(Λ-1) system and its curve shape are similar to that of the RNA-(Δ-1) system, suggesting that the binding modes of two enantiomers with RNA are intercalation. The obtained results in this work may be useful for understanding the binding differences in chiral Ru(II) polypyridyl complexes toward RNA triplex and duplex.

Chiral molecular imprinted sensor for highly selective determination of D-carnitine in enantiomers via dsDNA-assisted conformation immobilization

In this paper, a novel approach was established on the basis of a molecularly imprinted technique with the aid of double-stranded deoxyribonucleic acid (dsDNA) embedded in a molecularly imprinted polymer (MIP) membrane as a new functional unit with chiral recognition for highly specific chiral recognition. The chiral molecules were immobilized and anchored in the cavities of the MIP membrane on the basis of the three-dimensional structure of a molecule determined by the functional groups, spatial characterization of the cavities of MIPs, and the spatial orientation with dsDNA embedded in MIPs. D-carnitine was selected as an example of a chiral molecular template, which intercalated into dsDNA immobilized on the gold electrode surface to form dsDNA-D-carnitine complex, and then the complex was embedded in the MIP during electropolymerization. After elution, the stereo-selective cavities were obtained. Our findings have shown that AAAA-TTTT base sequence had high affinity for D-carnitine intercalation. Combined with the electrochemical detection method, MIP sensor was prepared. The selectivity of the MIP sensor to ultratrace D-carnitine was significantly improved; the sensor had remarkable stereo-selectivity and highly chiral specific recognition to D-carnitine, and L-carnitine with a concentration of 10,000 times D-carnitine did not interfere with the detection of D-carnitine in the assay of raceme. The sensor also exhibited high sensitivity to ultratrace D-carnitine determination with a linear response to the concentration of D-carnitine in the range of 3.0 × 10^-16 mol/L to 4.0 × 10^-13 mol/L, with a detection limit of 2.24 × 10^-16 mol/L. The mechanism of chiral recognition was studied, and result showed that apart from the recognition effect of imprinted cavities, dsDNA provided chiral selectivity to the spatial orientation of chiral molecules via the intercalation of chiral molecules with dsDNA and electrostatic interaction with groups of DNA base.

An 111In-labelled bis-ruthenium(ii) dipyridophenazine theranostic complex: mismatch DNA binding and selective radiotoxicity towards MMR-deficient cancer cells

Theranostic radionuclides that emit Auger electrons (AE) can generate highly localised DNA damage and the accompanying gamma ray emission can be used for single-photon emission computed tomography (SPECT) imaging. Mismatched DNA base pairs (mismatches) are DNA lesions that are abundant in cells deficient in MMR (mismatch mediated repair) proteins. This form of genetic instability is prevalent in the MMR-deficient subset of colorectal cancers and is a potential target for AE radiotherapeutics. Herein we report the synthesis of a mismatch DNA binding bis-ruthenium(ii) dipyridophenazine (dppz) complex that can be radiolabelled with the Auger electron emitting radionuclide indium-111 (111In). Greater stabilisation accompanied by enhanced MLCT (metal to ligand charge-transfer) luminescence of both the bis-Ru(dppz) chelator and non-radioactive indium-loaded complex was observed in the presence of a TT mismatch-containing duplex compared to matched DNA. The radioactive construct [111In]In-bisRu(dppz) ([111In][In-2]4+) targets cell nuclei and is radiotoxic towards MMR-deficient human colorectal cancer cells showing substantially less detrimental effects in a paired cell line with restored MMR function. Additional cell line studies revealed that [111In][In-2]4+ is preferentially radiotoxic towards MMR-deficient colorectal cancer cells accompanied by increased DNA damage due to 111In decay. The biodistribution of [111In][In-2]4+ in live mice was demonstrated using SPECT. These results illustrate how a Ru(ii) polypyridyl complex can incorporate mismatch DNA binding and radiometal chelation in a single molecule, generating a DNA-targeting AE radiopharmaceutical that displays selective radiotoxicity towards MMR-deficient cancer cells and is compatible with whole organism SPECT imaging.

Structural Basis for Targeting T:T Mismatch with Triaminotriazine-Acridine Conjugate Induces a U-Shaped Head-to-Head Four-Way Junction in CTG Repeat DNA

The potent DNA-binding compound triaminotriazine-acridine conjugate (Z1) functions by targeting T:T mismatches in CTG trinucleotide repeats that are responsible for causing neurological diseases such as myotonic dystrophy type 1, but its binding mechanism remains unclear. We solved a crystal structure of Z1 in a complex with DNA containing three consecutive CTG repeats with three T:T mismatches. Crystallographic studies revealed that direct intercalation of two Z1 molecules at both ends of the CTG repeat induces thymine base flipping and DNA backbone deformation to form a four-way junction. The core of the complex unexpectedly adopts a U-shaped head-to-head topology to form a crossover of each chain at the junction site. The crossover junction is held together by two stacked G:C pairs at the central core that rotate with respect to each other in an X-shape to form two nonplanar minor-groove-aligned G·C·G·C tetrads. Two stacked G:C pairs on both sides of the center core are involved in the formation of pseudo-continuous duplex DNA. Four metal-mediated base pairs are observed between the N7 atoms of G and Co^II, an interaction that strongly preserves the central junction site. Beyond revealing a new type of ligand-induced, four-way junction, these observations enhance our understanding of the specific supramolecular chemistry of Z1 that is essential for the formation of a noncanonical DNA superstructure. The structural features described here serve as a foundation for the design of new sequence-specific ligands targeting mismatches in the repeat-associated structures.

From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies

DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.

Dinuclear metal complexes: multifunctional properties and applications

Dinuclear metal complexes have enabled breakthroughs in OLEDs, photocatalytic water splitting and CO₂reduction, DSPEC, chemosensors, biosensors, PDT and smart materials.

Studies on the influence of the nuclearity of zinc(ii) hemi-salen complexes on some pivotal biological applications

Experimental and theoretical corroboration of the various biological applications of two nuclearity-dependent dimeric and trimeric Zn(ii) hemi-salen complexes.

Mechanism for the Binding of Netropsin to Hairpin DNA Revealed Using Nanoscale Ion Emitters in Native Mass Spectrometry

Netropsin is one of the first ligands to be discovered that selectively binds to the minor groove of DNA and is actively used as a scaffold for developing potential anticancer and antibiotic agents. The mechanism by which netropsin binds to hairpin DNA remains controversial with two competing mechanisms having been proposed. In one mechanism, netropsin binding induces a hairpin-to-duplex DNA transition. Alternatively, netropsin binds in two thermodynamically different modes at a single duplexed AATT site. Here, results from native mass spectrometry (MS) with nanoscale ion emitters indicate that netropsin can simultaneously and sequentially bind to both hairpin and duplex DNA. Duplex DNA was not detected using conventional MS with larger emitters because nanoscale emitters significantly reduce the extent of salt adduction to ligand-DNA complex ions, including in the presence of relatively high concentrations of nonvolatile salts. Based on native MS and polyacrylamide gel electrophoresis results, the abundances of hairpin and duplex DNA are unaffected by the addition of netropsin. By native MS, the binding affinities for five ligand-DNA and DNA-DNA interactions can be rapidly obtained simultaneously. This research indicates a "simultaneous binding mechanism" for the interactions of netropsin with DNA.

Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation

DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic Co^II(Chro)₂ (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.