Iridium(III)-based minor groove binding complexes as DNA photocleavage agents

Transition metal complexes containing the qtpy ligand (2':4,4'':4',4'''-quaterpyridyl) are known to be DNA intercalators or minor groove binders. In this study, new tricationic iridium(III) complexes of qtpy are reported. Both [Ir(bpy)2(qtpy)]3+1 and [Ir(phen)2(qtpy)]3+2 display good water solubility as chloride salts. The complexes possess high-energy excited states, which are quenched in the presence of duplex DNA and even by the mononucleotides guanosine monophosphate and adenosine monophosphate. Further studies reveal that although the complexes bind to quadruplex DNA, they display a preference for duplex structures, which are bound with an order of magnitude higher affinities than their isostructural dicationic RuII-analogues. Detailed molecular dynamics simulations confirm that the complexes are groove binders through the insertion of, predominantly, the qtpy ligand into the minor groove. Photoirradiation of 1 in the presence of plasmid DNA confirms that this class of complexes can function as synthetic photonucleases by cleaving DNA.

Photoactivatable, mitochondria targeting dppz iridium(III) complex selectively interacts and damages mitochondrial DNA in cancer cells

Cyclometalated Ir(III) complex [Ir(L)2(dppz)]PF6 (where L = 1-methyl-2-(thiophen-2-yl)-1H-benzo[d]imidazole and dppz = dipyrido [3,2-a:2',3'-c]phenazine) (Ir1) is potent anticancer agent whose potency can be significantly increased by irradiation with blue light. Structural features of the cyclometalated Ir(III) complex Ir1 investigated in this work, particularly the presence of dppz ligand possessing an extended planar area, suggest that this complex could interact with DNA. Here, we have shown that Ir1 accumulates predominantly in mitochondria of cancer cells where effectively and selectively binds mitochondrial (mt)DNA. Additionally, the results demonstrated that Ir1 effectively suppresses transcription of mitochondria-encoded genes, especially after irradiation, which may further affect mitochondrial (and thus also cellular) functions. The observation that Ir1 binds selectively to mtDNA implies that the mechanism of its biological activity in cancer cells may also be connected with its interaction and damage to mtDNA. Further investigations revealed that Ir1 tightly binds DNA in a cell-free environment, with sequence preference for GC over AT base pairs. Although the dppz ligand itself or as a ligand in structurally similar DNA-intercalating Ru polypyridine complexes based on dppz ligand intercalates into DNA, the DNA binding mode of Ir1 comprises surprisingly a groove binding rather than an intercalation. Also interestingly, after irradiation with visible (blue) light, Ir1 was capable of cleaving DNA, likely due to the production of superoxide anion radical. The results of this study show that mtDNA damage by Ir1 plays a significant role in its mechanism of antitumor efficacy. In addition, the results of this work are consistent with the hypothesis and support the view that targeting the mitochondrial genome is an effective strategy for anticancer (photo)therapy and that the class of photoactivatable dipyridophenazine Ir(III) compounds may represent prospective substances suitable for further testing.

Bifunctional ruthenium(ii) polypyridyl complexes of curcumin as potential anticancer agents

Ru(ii)-polypyridyl complexes have been widely studied and well established for their antitumor properties. Modifications of the coordination environment around the Ru atom through a proper choice of the ligand can lead to different modes of action and result in greatly improved anticancer efficacy. Herein, two Ru(ii)-polypyridyl complexes of curcumin were synthesized and characterized as potential anticancer agents. In vitro tests indicated that complexes 1 and 2 displayed excellent antiproliferative activity against the tested cancer cell lines, especially complex 2, which exhibited superior cytotoxicity compared to curcumin and cisplatin. Further biological evaluations demonstrated that complexes 1 and 2 can cause cell apoptosis via DNA interaction and MEK/ERK signaling pathway, which is the first example of a Ru(ii)-polypyridyl complex inhibiting the MEK/ERK signaling pathway and DNA intercalation. Overall, this work suggests that coordination with bioactive agents may endow Ru(ii)-polypyridyl complexes with improved pharmaceutical properties and synergistic effects for cancer therapy.

Canonical DNA minor groove insertion of bisbenzamidine-Ru(ii) complexes with chiral selectivity

We report the first Ru(ii) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis-benzamidine minor groove DNA-binding agent with a ruthenium(ii) complex. Importantly, one of the enantiomers (Δ-[Ru(bpy)2 b4bpy]2+, Δ-4Ru) shows a considerably higher DNA affinity than the parent organic ligand and the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.

DNA directed damage using a brominated DAPI derivative

Conversion of a DNA-binding fluorophore (DAPI) to a photosensitizer via bromination retains high fluorescence and high affinity DNA binding but now produces light-induced reactive oxygen species directed towards DNA resulting in rapid cancer cell death.

Turning intercalators into groove binders: synthesis, photophysics and DNA binding properties of tetracationic mononuclear ruthenium(ii)-based chromophore–quencher complexes

Despite incorporating an extended planar polyaromatic ligand two newly synthesized Ru^II complexes are not DNA intercalators but groove binders.

Microwave-assisted one-pot synthesis of new ionic iridium complexes of [Ir(bzq)2(N^N)]+A- type and their selected electroluminescent properties

Iridium C,N-cyclometalated complexes with an ionic structure are considered to be promising candidates for application in host/guest solid-state phosphorescent single-layer devices because the employment of such dopants offers the possibility of reducing their concentration in organic matrices as well as allows obtaining organic light emitting devices (OLEDs) with interesting emission parameters. We report herein a methodology enabling the synthesis of cyclometalated ionic iridium(iii) complexes of the type [Ir(C^N)₂(N^N)]⁺A^- according to a three-component one-pot strategy involving the acceleration of the reaction via microwave irradiation. The developed protocol allowed efficient synthesis of a series of new cationic iridium(iii) coordination derivatives, which were isolated and spectroscopically characterized, while the structures of two of them were determined by the X-ray method. Moreover, the iridium(iii) derivatives were subjected to the cyclic voltammetry studies in order to determine the energies of the HOMO and LUMO levels as well as to estimate their electrochemical properties and to predict some electronic properties. Additionally, the ONIOM calculation scheme that was used to predict HOMO-LUMO gaps for the studied Ir(iii) complexes showed a good correlation between the experimental and calculated values. In order to determine the influence of the structure and nature of the ancillary ligand on the location of the maximum emission band, the photophysical properties of the synthesized iridium complexes were characterized. Finally, the selected compounds were used as emitters for the construction of polymer light emitting diodes (PLEDs) based on a poly(N-vinylcarbazole)/2-(4-tert-butylphenyl)-5-(4-biphenyl)-1,3,4-oxadiazole (PVK/PBD) matrix. The highest luminance, above 10 000 cd m^-2, was recorded for the device containing only 1.0 wt% of [Ir(bzq)₂(1,10-phenanthroline)]⁺PF₆^- in the PVK/PBD. The fabricated PLEDs exhibit current efficiency in the range of 1.0 to 2.2 cd A^-1.

A ratiometric sensor for DNA based on a dual emission Ru(dppz) light-switch complex

Herein we describe the DNA binding properties of two new water-soluble ruthenium complexes; experimental and computational data reveal that both complexes display dual emission from MLCT and LLCT excited states.

Utilization of Electrochromically Luminescent Transition-Metal Complexes for Erasable Information Recording and Temperature-Related Information Protection

Transition metal complexes containing pyrazinium or pyridinium moieties display reversible luminescence changes in response to electrical stimuli, which is useful in the development of erasable information recording electric devices. These complexes are also suitable for temperature-related information protection, since chemically-induced luminescence turn-on is temperature-dependent.

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their K_i, K_d, IC₅₀ values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php.

Database URL:http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php

A tale of two paralogs: human Transformer2 proteins with differential RNA-binding affinities

The Transformer2 (Tra2) proteins in humans are homologues of the Drosophila Tra2 protein. One of the two RNA-binding paralogs, Tra2β, has been very well-studied over the past decade, but not much is known about Tra2α. It was very recently shown that the two proteins demonstrate the phenomenon of paralog compensation. Here, we provide a structural basis for this genetic backup circuit, using molecular modelling and dynamics studies. We show that the two proteins display similar binding specificities, but differential affinities to a short GAA-rich RNA stretch. Starting from the 6-nucleotide RNA in the solution structure, close to 4000 virtual mutations were modelled on RNA and the domain-RNA interactions were studied after energy minimisation to convergence. Separately, another known 13-nucleotide stretch was docked and the domain-RNA interactions were observed through a 100-ns dynamics trajectory. We have also demonstrated the 'compensatory' mechanism at the level of domains in one of the domain repeat-containing RNA-binding proteins.

Crystal structure of [1,1'''-bis-(pyrimidin-2-yl)-4,4':2',2'':4'',4'''-quaterpyridine-1,1'''-diium-κ(2) N (1'),N (1'')]bis-[2-(pyridin-2-yl)phenyl-κ(2) N,C (1)]iridium(III) tris-(hexa-fluorido-phosphate) aceto-nitrile tris-olvate

In the title compound, [Ir(C11H8N)2(C28H20N8)](PF6)3·3CH3CN or [Ir(III)(ppy)2{(2-pym)2qpy(2+)}](PF6)3·3CH3CN (ppy = deprotonated 2-phenyl-pyridine, pym = pyrimidyl and qpy = 4,4':2',2'':4'',4'''-quaterpyrid-yl), the Ir(3+) cation is coordinated by two C atoms and four N atoms in a slightly distorted octa-hedral geometry. The asymmetric unit consists of one complex trication, three hexa-fluorido-phosphate anions and three aceto-nitrile solvent mol-ecules. The average Ir-C distance is 2.011 (14) Å, the average Ir-N(ppy) distance is 2.05 (6) Å and the average Ir-N(qpy) distance is longer at 2.132 (10) Å. The dihedral angles within the 4,4'-bipyridyl units are 31.5 (6) and 23.8 (7)°, while those between the 2-pym and attached pyridyl rings are rather smaller, at 11.7 (9) and 7.1 (9)°. The title compound was refined as a two-component inversion twin.

‘Aggregation induced phosphorescence’ active iridium(iii) complexes for integrated sensing and inhibition of bacterial growth in aqueous solution

The present study attempts to develop a sensitive method to utilize ‘aggregation induced emission (AIE)’ active iridium(iii) complexes as potential agents for “integrated” sensing and inhibition of bacterial growth in aqueous systems.

Water-soluble Ir(iii) complexes of deprotonated N-methylbipyridinium ligands: fluorine-free blue emitters

Using the cation 1-methyl-3-(2′-pyridyl)pyridinium to produce cyclometalating ligands gives novel Ir^III complex salts that are water-soluble and emit efficiently blue or blue-green light.