Crystal structures of Λ-[Ru(phen)₂dppz]²⁺ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes

Luminescent ruthenium polypyridyl complexes with extended ‘dppz’ like ligands as DNA targeting binders and cellular agents

DNA-binding and phototoxicity of Ru(ii) complexes with ligands derived from pyrazinodipyridophenazine and either phen or TAP as ancillary ligands are reported.

Development of ruthenium-based complexes as anticancer agents: toward a rational design of alternative receptor targets

In the search for novel anticancer agents, the development of metal-based complexes that could serve as alternatives to cisplatin and its derivatives has received considerable attention in recent years. This becomes necessary because, at present, cisplatin and its derivatives are the only coordination complexes being used as anticancer agents in spite of inherent serious side effects and their limitation against metastasized platinum-resistant cancer cells. Although many metal ions have been considered as possible alternatives to cisplatin, the most promising are ruthenium (Ru) complexes and two Ru compounds, KP1019 and NAMI-A, which are currently in phase II clinical trials. The major obstacle against the rational design of these compounds is the fact that their mode of action in relation to their therapeutic activities and selectivity is not fully understood. There is an urgent need to develop novel metal-based anticancer agents, especially Ru-based compounds, with known mechanism of actions, probable targets, and pharmacodynamic activity. In this paper, we review the current efforts in developing metal-based anticancer agents based on promising Ru complexes and the development of compounds targeting receptors and then examine the future prospects.

Ruthenium(ii) complexes with dppz: from molecular photoswitch to biological applications

The present article describes the recent advances in biological applications of the Ru-dppz systems in DNA binding, cellular imaging, anticancer drugs, phototherapy, protein aggregation detecting and chemosensors.

Photoinduced interactions of two dirhodium complexes with d(GTCGAC)2 probed by 2D NOESY

The interactions between the 6-mer duplex oligonucleotide d(GTCGAC)2 and the photoactive dirhodium complexes cis-H,H-[Rh2(HNOCCH3)2(L)(CH3CN)4](2+), where L represents bpy (1, 2,2'-bipyridine) and dppz (2, dipyrido[3,2-a:2',3'-c]phenazine), were probed using 2D (1)H-(1)H NOESY NMR spectroscopy. Complex does not interact with the duplex in the dark, but binds covalently to the terminal guanine following irradiation with visible light. Similar behavior was observed for 2, but in addition to the photoinduced covalent DNA binding, the planar dppz ligand of the complex shields the terminal cytosine protons after irradiation. The results are consistent with photoinduced guanine coordination and end-capping of the duplex through π-stacking interactions with the terminal GC base pair. These data show that in the presence of the 6-mer duplex oligonucleotide, 1 and 2 exhibit photoinduced covalent binding to DNA. In addition, the π-stacking interactions of 2 with the duplex are enhanced upon irradiation.

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

DNA gated photochromism and fluorescent switch in a thiazole orange modified diarylethene

Thiazole orange-modified diarylethene (1) shows weak fluorescence but no photochromism in aqueous solution. When binding with DNA, the fluorescence of 1 is enhanced drastically and the photochromic reactivity is unlocked. This kind of DNA-responsive photoswitchable system can be used for imaging nucleic acids within cells.

Serum Albumin Binding Inhibits Nuclear Uptake of Luminescent Metal-Complex-Based DNA Imaging Probes

The DNA binding and cellular localization properties of a new luminescent heterobimetallic Ir(III) Ru(II) tetrapyridophenazine complex are reported. Surprisingly, in standard cell media, in which its tetracationic, isostructural Ru(II) Ru(II) analogue is localized in the nucleus, the new tricationic complex is poorly taken up by live cells and demonstrates no nuclear staining. Consequent cell-free studies reveal that the Ir(III) Ru(II) complex binds bovine serum albumin, BSA, in Sudlow's Site I with a similar increase in emission and binding affinity to that observed with DNA. Contrastingly, in serum-free conditions the complex is rapidly internalized by live cells, where it localizes in cell nuclei and functions as a DNA imaging agent. The absence of serum proteins also greatly alters the cytotoxicity of the complex, where high levels of oncosis/necrosis are observed due to this enhanced uptake. This suggests that simply increasing the lipophilicity of a DNA imaging probe to enhance cellular uptake can be counterproductive as, due to increased binding to serum albumin protein, this strategy can actually disrupt nuclear targeting.

Binding Behaviors for Different Types of DNA G-Quadruplexes: Enantiomers of [Ru(bpy)2(L)](2+) (L=dppz, dppz-idzo)

Polymorphic DNA G-quadruplex recognition has attracted great interest in recent years. The strong binding affinity and potential enantioselectivity of chiral [Ru(bpy)2 (L)](2+) (L=dipyrido[3,2-a:2',3'-c]phenazine, dppz-10,11-imidazolone; bpy=2,2'-bipyridine) prompted this investigation as to whether the two enantiomers, Δ and Λ, can show different effects on diverse structures with a range of parallel, antiparallel and mixed parallel/antiparallel G-quadruplexes. These studies provide a striking example of chiral-selective recognition of DNA G-quadruplexes. As for antiparallel (tel-Na(+)) basket G-quadruplex, the Λ enantiomers bind stronger than the Δ enantiomers. Moreover, the behavior reported here for both enantiomers stands in sharp contrast to B-DNA binding. The chiral selectivity toward mixed parallel/antiparallel (tel-K(+)) G-quadruplex of both compounds is weak. Different loop arrangements can change chiral complex selectivity for both antiparallel and mixed parallel/antiparallel G-quadruplex. Whereas both Δ and Λ isomers bind to parallel G-quadruplexes with comparable affinity, no appreciable stereoselective G-quadruplex binding of the isomers was observed. In addition, different binding stoichiometries and binding modes for Δ and Λ enantiomers were confirmed. The results presented here indicate that chiral selective G-quadruplex binding is not only related to G-quadruplex topology, but also to the sequence and the loop constitution.

Reversal of a Single Base-Pair Step Controls Guanine Photo-Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo‐oxidation by Λ‐[Ru(TAP)₂(dppz)]²⁺ have been compared in 5′‐{CCGGATCCGG}₂ and 5′‐{CCGGTACCGG}₂ using pico/nanosecond transient visible and time‐resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′‐TA‐3′ versus 5′‐AT‐3′ binding preference predicted by X‐ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.

Detailed Biological Profiling of a Photoactivated and Apoptosis Inducing pdppz Ruthenium(II) Polypyridyl Complex in Cancer Cells

Ruthenium polypyridyl complexes show great promise as new photodynamic therapy (PDT) agents. However, a lack of detailed understanding of their mode of action in cells poses a challenge to their development. We have designed a new Ru(II) PDT candidate that efficiently enters cells by incorporation of the lipophilic aromatic pdppz ([2,3-h]dipyrido[3,2-a:2',3'-c]phenazine) ligand and exhibits photoactivity through incorporation of 1,4,5,8-tetraazaphenanthrene ancillary ligands. Its photoreactivity toward biomolecules was studied in vitro, where light activation caused DNA cleavage. Cellular internalization occurred via an energy dependent mechanism. Confocal and transmission electron microscopy revealed that the complex localizes in various organelles, including the mitochondria. The complex is nontoxic in the dark, with cellular clearance within 96 h; however, upon visible light activation it induces caspase-dependent and reactive-oxygen-species-dependent apoptosis, with low micromolar IC50 values. This investigation greatly increases our understanding of such systems in cellulo, aiding development and realization of their application in cancer therapy.

Supramolecular activation of a molecular photocatalyst

The effects of the planar aromatic organic molecules anthracene and pyrene on the catalytic performance of the intramolecular hydrogen evolving photocatalyst [Ru(tbbpy)2(tpphz)PdCl2](PF6)2 functioning as a photocatalytic dyad have been studied. (1)H-NMR studies on [Ru(tbbpy)2(tpphz)PdCl2](PF6)2 and [Ru(tbbpy)2(tpphz)](PF6)2 show a pronounced interaction of pyrene with the ruthenium complexes due to π-π-interactions. The solid state structure of [Ru(tbbpy)2(tpphz)PdCl2]2[Mo8O24] shows a pronounced π-π-stacking of the polyaromatic ligands. In addition, dimerization constants for the complexes and association constants between the complexes and pyrene were determined. Studies on the photocatalytic hydrogen production show a decreased induction phase and increased turn over frequencies during the initial phase of the catalysis in the presence of anthracene and pyrene utilising the catalyst [Ru(tbbpy)2(tpphz)PdCl2](PF6)2 irrespective of the nature of the polycyclic aromatic hydrocarbon.

Expanding the family of heteroleptic oxidovanadium(IV) compounds with salicylaldehyde semicarbazones and polypyridyl ligands showing anti-Trypanosoma cruzi activity

Searching for prospective vanadium-based drugs for the treatment of Chagas disease, a new series of heteroleptic [V(IV)O(L-2H)(NN)] compounds was developed by including the lipophilic 3,4,7,8-tetramethyl-1,10-phenanthroline (tmp) NN ligand and seven tridentate salicylaldehyde semicarbazone derivatives (L1-L7). The compounds were characterized in the solid state and in solution. EPR spectroscopy suggests that the NN ligand is bidentate bound through both nitrogen donor atoms in an axial-equatorial mode. The EPR and (51)V-NMR spectra of aerated solutions at room temperature indicate that the compounds are stable to hydrolysis and that no significant oxidation of V(IV) to V(V) takes place at least in 24h. The complexes are more active in vitro against Trypanosoma cruzi, the parasite responsible for Chagas disease, than the reference drug Nifurtimox and most of them are more active than previously reported [V(IV)O(L-2H)(NN)] complexes of other NN co-ligands. Selectivity towards the parasite was analyzed using J-774 murine macrophages as mammalian cell model. Due to both, high activity and high selectivity, L2, L4, L5 and L7 complexes could be considered new hits for further drug development. Lipophilicity probably plays a relevant role in the bioactivity of the new compounds. The [V(IV)O(L-2H)(NN)] compounds were designed aiming DNA as potential molecular target. Therefore, the novel L1-L7 tmp complexes were screened by computational modeling, comparing their DNA-binding features with those of previously reported [V(IV)O(L-2H)(NN)] compounds with different NN co-ligands. Whereas all the complexes interact well with DNA, with binding modes and strength tuned in different extents by the NN and semicarbazone co-ligands, molecular docking suggests that the observed anti-T. cruzi activity cannot be explained upon DNA intercalation as the sole mechanism of action.

Enantiomeric Conformation Controls Rate and Yield of Photoinduced Electron Transfer in DNA Sensitized by Ru(II) Dipyridophenazine Complexes

Photosensitized oxidation of guanine is an important route to DNA damage. Ruthenium polypyridyls are very useful photosensitizers, as their reactivity and DNA-binding properties are readily tunable. Here we show a strong difference in the reactivity of the two enantiomers of [Ru(TAP)2(dppz)](2+), by using time-resolved visible and IR spectroscopy. This reveals that the photosensitized one-electron oxidation of guanine in three oligonucleotide sequences proceeds with similar rates and yields for bound Δ-[Ru(TAP)2(dppz)](2+), whereas those for the Λ enantiomer are very sensitive to base sequence. It is proposed that these differences are due to preferences of each enantiomer for different binding sites in the duplex.

Syntheses and properties of phosphine-substituted ruthenium(ii) polypyridine complexes with nitrogen oxides

The substitution lability of the nitrogen oxide ligands of novel phosphine-substituted ruthenium(ii) polypyridine complexes is discussed in comparison with that of the corresponding acetonitrile complexes.

Microwave-Assisted Synthesis of Ruthenium(II) Complexes with Trimethylsilylacetylene as Inhibitors against the Migration of Breast Cancer Cells

In the present study, two novel chiral ruthenium(ii) complexes with trimethylsilylacetylene (TMSA), Λ- and Δ-[Ru(bpy)2(p-TEPIP)](ClO4)2 (bpy = 2,2-bipyridine; p-TEPIP = 5-(2-(p-trimethylsilyl propargyl)-1H-imidazo[4,5-f][1,10] phenanthroline) (Λ-1 and Δ-1) were prepared using Sonogashira coupling reaction under microwave irradiation. We found that both Λ-1 and Δ-1 could inhibit the growth of highly metastatic human breast cancer cells (MDA-MB-231) with half-maximal inhibitory concentration (IC50) of 32.1 and 36.9 µM, respectively. Wound healing assay demonstrated that both isomers inhibited the migration of MDA-MB-231 cells. Both Λ-1 and Δ-1 compounds were found throughout the cell and were particularly enriched in the nucleus. Furthermore, we observed fragmentation of the nucleus leading to apoptosis. To conclude, it is clear that this type of chiral ruthenium(ii) complex with TMSA can induce apoptosis and thus inhibit the growth and migration of tumour cells.

Unexpected DNA binding properties with correlated downstream biological applications in mono vs. bis-1,8-naphthalimide Ru(ii)-polypyridyl conjugates

The development of two 1,8-napthalimide-conjugated Ru(ii)-polypyridyl complexes which exhibit different DNA binding and photocleavage behavior is presented.

Control and utilization of ruthenium and rhodium metal complex excited states for photoactivated cancer therapy

The use of visible light to produce highly selective and potent drugs through photodynamic therapy (PDT) holds much potential in the treatment of cancer. PDT agents can be designed to follow an O2-dependent mechanism by producing highly reactive species such as 1O2 and/or an O2 independent mechanism through processes such as excited state electron transfer, covalent binding to DNA or photoinduced drug delivery. Ru(II)-polypyridyl and Rh2(II,II) complexes represent an important class of compounds that can be tailored to exhibit desired photophysical properties and photochemical reactivity by judicious selection of the ligand set. Complexes with relatively long-lived excited states and planar, intercalating ligands localize on the DNA strand and photocleave DNA through 1O2 production or guanine oxidation by the excited state of the chromophore. Photoinduced ligand substitution occurs through the population of triplet metal centered (3MC) excited states and facilitates covalent binding of the metal complex to DNA in a mode similar to cisplatin. Ligand photodissociation also provides a route to selective drug delivery. The ability to construct metal complexes with desired light absorbing and excited state properties by ligand variation enables the design of PDT agents that can potentially provide combination therapy from a single metal complex.

Impacts of terminal modification of [Ru(phen)2dppz]2+on the luminescence properties: a theoretical study

Lowest singlet transitions were found to be related to the intriguing luminescence properties of three different dppz-like ruthenium(ii) complexes through a theoretical study.

Binding of Ru(terpyridine)(pyridine)dipyridophenazine to DNA studied with polarized spectroscopy and calorimetry

Achiral Ru(tpy)(py)dppz²⁺ intercalated into DNA has similar intermolecular interactions as opposite enantiomers of its structural isomer, the “light-switch” complex Ru(bpy)₂dppz²⁺.

Controlled dehydration of a ruthenium complex-DNA crystal induces reversible DNA kinking

Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven data sets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.

Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex

DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)₄Ru₂]⁴⁺ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation K_d is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.

Ruthenium polypyridine complexes combined with oligonucleotides for bioanalysis: a review

Ruthenium complexes are among the most interesting coordination complexes and they have attracted great attention over the past decades due to their appealing biological, catalytic, electronic and optical properties. Ruthenium complexes have found a unique niche in bioanalysis, as demonstrated by the substantial progress made in the field. In this review, the applications of ruthenium complexes coordinated with polypyridine ligands (and analogues) in bioanalysis are discussed. Three main detection methods based on electrochemistry, electrochemiluminescence, and photoluminscence are covered. The important targets, including DNA and other biologically important targets, are detected by specific biorecognition with the corresponding oligonucleotides as the biorecognition elements (i.e., DNA is probed by its complementary strand and other targets are detected by functional nucleic acids, respectively). Selected examples are provided and thoroughly discussed to highlight the substantial progress made so far. Finally, a brief summary with perspectives is included.

In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27

New features of an antiprotozoal DNA minor-groove binding drug, which acts as a cross-linking agent, are presented. It also fills the minor groove of DNA completely and prevents the access of proteins. These features are also expected for other minor-groove binding drugs when associated with suitable DNA targets.

The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice. Previous studies have been performed almost exclusively with the AATT sequence. New features should be uncovered through the study of different DNA sequences. In this paper, the crystal structure of the complex of the DNA duplex d(AAAATTTT)₂ with the dicationic drug 4,4′-bis(imidazolinylamino)diphenylamine (CD27) is presented. The drug binds to the minor groove of DNA as expected, but it shows two new features that have not previously been described: (i) the drugs protrude from the DNA and interact with neighbouring molecules, so that they may act as cross-linking agents, and (ii) the drugs completely cover the whole minor groove of DNA and displace bound water. Thus, they may prevent the access to DNA of proteins such as AT-hook proteins. These features are also expected for other minor-groove binding drugs when associated with all-AT DNA. These findings allow a better understanding of this family of compounds and will help in the development of new, more effective drugs. New data on the biological interaction of CD27 with the causative agent of trichomoniasis, Trichomonas vaginalis, are also reported.

A novel type of coordination mode of chloranilic acid leading to the formation of polymeric coordination ribbon in the series of mixed-ligand copper(II) complexes with 1,10-phenanthroline

A series of four novel mixed-ligand complexes of copper(II) with 3,6-dichloro-2,6-dihydroxy-1,4-benzoquinone (chloranilic acid) and 1,10-phenanthroline was prepared and characterised by X-ray structure analysis and IR spectroscopy. Three complexes exhibit square-pyramidal coordination, whereas one exhibits octahedral coordination. The ligand 1,10-phenanthroline acts in a bidentate chelating mode with N,N-metal binding. The chloranilate dianion coordinates to the Cu(II) atom in a terminal bidentate ortho-quinone-like mode, forming a mononuclear complex species. However, in one structure a novel type of coordination mode of chloranilate is observed. In addition to the bidentate mode, a monodentate bridging mode through a carboxy oxygen of a symmetry-related dianion leads to the formation of polymeric coordination ribbon. The crystal packing of penta-coordinated species, in addition to hydrogen bonding, involves less common stacking interactions of chelate rings with the π-systems of the ligands.

RutheniumII complexes bearing fused polycyclic ligands: from fundamental aspects to potential applications

In this review, we first discuss the photophysics reported in the literature for mononuclear ruthenium complexes bearing ligands with extended aromaticity such as dipyrido[3,2-a:2',3'-c]phenazine (DPPZ), tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]-phenazine (TPPHZ),  tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]acridine (TPAC), 1,10-phenanthrolino[5,6-b]1,4,5,8,9,12-hexaazatriphenylene (PHEHAT) 9,11,20,22-tetraaza- tetrapyrido[3,2-a:2',3'-c:3'',2''-l:2''',3'''-n]pentacene (TATPP), etc. Photophysical properties of binuclear and polynuclear complexes based on these extended ligands are then reported. We finally develop the use of binuclear complexes with extended π-systems for applications such as photocatalysis.

Gold(III) macrocycles: nucleotide-specific unconventional catalytic inhibitors of human topoisomerase I

Topoisomerase IB (Top1) is a key eukaryotic nuclear enzyme that regulates the topology of DNA during replication and gene transcription. Anticancer drugs that block Top1 are either well-characterized interfacial poisons or lesser-known catalytic inhibitor compounds. Here we describe a new class of cytotoxic redox-stable cationic Au³⁺ macrocycles which, through hierarchical cluster analysis of cytotoxicity data for the lead compound, 3, were identified as either poisons or inhibitors of Top1. Two pivotal enzyme inhibition assays prove that the compounds are true catalytic inhibitors of Top1. Inhibition of human topoisomerase IIα (Top2α) by 3 was 2 orders of magnitude weaker than its inhibition of Top1, confirming that 3 is a type I-specific catalytic inhibitor. Importantly, Au³⁺ is essential for both DNA intercalation and enzyme inhibition. Macromolecular simulations show that 3 intercalates directly at the 5′-TA-3′ dinucleotide sequence targeted by Top1 via crucial electrostatic interactions, which include π–π stacking and an Au···O contact involving a thymine carbonyl group, resolving the ambiguity of conventional (drug binds protein) vs unconventional (drug binds substrate) catalytic inhibition of the enzyme. Surface plasmon resonance studies confirm the molecular mechanism of action elucidated by the simulations.

Study of picosecond processes of an intercalated dipyridophenazine Cr(iii) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods

Excited-state quenching of DNA intercalated [Cr(phen)₂(dppz)]³⁺ by guanine proceeds by rapid forward and back electron transfer of <3 ps.