Targeting topoisomerase II with the chiral DNA-intercalating ruthenium(II) polypyridyl complexes

From Intercalation to External Binding: Ru(II) Complexes with a Spiro Ligand for TAR RNA Selective Binding and HIV-1 Reverse Transcriptase Inhibition

As a typical RNA virus, the genetic information on HIV-1 is entirely stored in RNA. The reverse transcription activity of HIV-1 reverse transcriptase (RT) plays a crucial role in the replication and transmission of the virus. Non-nucleoside RT inhibitors (NNRTIs) block the function of RT by binding to the RNA binding site on RT, with very few targeting viral RNA. In this study, by transforming planar conjugated ligands into a spiro structure, we convert classical Ru(II) DNA intercalators into a nonintercalator. This enables selective binding to HIV-1 transactivation response (TAR) RNA on the outer side of nucleic acids through dual interactions involving hydrogen bonds and electrostatic attraction, effectively inhibiting HIV-1 RT and serving as a selective fluorescence probe for TAR RNA.

Bithiophene-Functionalized Infrared Two-Photon Absorption Metal Complexes as Single-Molecule Platforms for Synergistic Photodynamic, Photothermal, and Chemotherapy

A planar conjugated ligand functionalized with bithiophene and its Ru(II), Os(II), and Ir(III) complexes have been constructed as single-molecule platform for synergistic photodynamic, photothermal, and chemotherapy. The complexes have significant two-photon absorption at 808 nm and remarkable singlet oxygen and superoxide anion production in aqueous solution and cells when exposed to 808 nm infrared irradiation. The most potent Ru(II) complex Ru7 enters tumor cells via the rare macropinocytosis, locates in both nuclei and mitochondria, and regulates DNA-related chemotherapeutic mechanisms intranuclearly including DNA topoisomerase and RNA polymerase inhibition and their synergistic effects with photoactivated apoptosis, ferroptosis and DNA cleavage. Ru7 exhibits high efficacy in vivo for malignant melanoma and cisplatin-resistant non-small cell lung cancer tumors, with a 100 % survival rate of mice, low toxicity to normal cells and low residual rate. Such an infrared two-photon activatable metal complex may contribute to a new generation of single-molecule-based integrated diagnosis and treatment platform to address drug resistance in clinical practice and phototherapy for large, deeply located solid tumors.

Peroxidase-like oxidative activity of cobalt-based 1D coordination polymer; experimental and theoretical investigations

CONTEXT

The present work describes the synthesis, structural characterization, and catalytic activity of a Co(II)-based one-dimensional coordination polymer (CP1). To validate the chemotherapeutic potential of CP1, in vitro DNA binding assessment was carried out by employing multispectroscopic techniques. Moreover, the catalytic activity of CP1 was also ascertained during the oxidative conversion of o-phenylenediamine (OPD) to diaminophenazine (DAP) under aerobic conditions.

METHODS

The molecular structure of CP1 was solved with the olex2.solve structure solution program using charge flipping and refined with the olex2.refine refinement package by using Gauss-Newton minimization. The DFT studies were performed by utilizing ORCA Program Version 4.1.1 to calculate the electronic and chemical properties of CP1 by calculating the HOMO-LUMO energy gap. All calculations were carried out at B3LYP hybrid functional using def2-TZVP as the basis set. Contour plots of various FMOs were visualized by using Avogadro software. Hirshfeld surface analysis was carried out by Crystal explorer Program 17.5.27 to examine the various non-covalent interactions which are crucial for the stability of crystal lattice. In addition, molecular docking studies of CP1 with DNA were performed by using AutoDock Vina software and AutoDock tools (version 1.5.6). Discovery studio 3.5 Client 2020 was used for visualization of the docked pose and binding interactions of CP1 with ct-DNA.

Biophysical insights into the interaction of two enantiomers of Ru(II) complex [Ru(bpy)2(7-CH3-dppz)]2+ with the RNA poly(U-A⁎U) triplex

To determine the factors affecting the stabilization of RNA triple-stranded structure by chiral Ru(II) polypyridyl complexes, a new pair of enantiomers, ∆-[Ru(bpy)₂(7-CH₃-dppz)]²⁺ (∆-1; bpy = 2,2'-bipyridine, 7-CH₃-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) and Λ-[Ru(bpy)₂(7-CH₃-dppz)]²⁺ (Λ-1), have been synthesized and characterized in this work. Binding properties of the two enantiomers with the RNA poly(U-A⁎U) triplex (where "-" denotes the Watson - Crick base pairing and "⁎" denotes the Hoogsteen base pairing) have been studied by spectroscopy and hydrodynamics methods. Under the conditions used in this study, changes in absorption spectra of the two enantiomers are not very different from each other when bound to the triplex, although the binding affinity of ∆-1 is higher than that of Λ-1. Fluorescence titrations and viscosity experiments give convincing evidence for a true intercalative binding of enantiomers with the triplex. However, melting experiments indicated that the two enantiomers selectively stabilized the triplex. The enantiomer ∆-1 stabilize the template duplex and third-strand of the triplex, while it's more effective for stabilization of the template duplex. In stark contrast to ∆-1, Λ-1 stabilizes the triplex without any effect on the third-strand stabilization, suggesting this one extremely prefers to stabilize the template duplex rather than third-strand. Besides, the triplex stabilization effect of ∆-1 is more marked in comparison with that of Λ-1. The obtained results suggest that substituent effects and chiralities of Ru(II) polypyridyl complexes play important roles in the triplex stabilization. Complexes Λ/Δ-[Ru(bpy)₂(7-CH₃-dppz)]²⁺ (Λ/Δ-1; bpy = 2,2'-bipyridine, 7-CH₃-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) were prepared as stabilizers for poly(U-A ∗ U) triplex. Results suggest the triplex stabilization depends the chiral structures of Λ/Δ-1, indicating that [Ru(bpy)₂(7-CH₃-dppz)]²⁺ is a non-specific intercalator for poly(U-A ∗ U) investigated in this work.

Design and synthesis of a DNA intercalative half-sandwich organoruthenium(ii)–chromone complex: cytotoxicity evaluation and topoisomerase Iα inhibition assay

A half-sandwich organoruthenium(ii)–chromone complex acts as a potential topoisomerase I inhibitor.

Non-mutagenic Ru(ii) complexes: cytotoxicity, topoisomerase IB inhibition, DNA and HSA binding

Herein we discuss five ruthenium(ii) complexes with good cytotoxicity against cancer cells.

Carbohydrate-based heteronuclear complexes as topoisomerase Iα inhibitor: approach toward anticancer chemotherapeutics

Due to the critical role of cellular enzymes necessary for cell proliferation by deciphering topological hurdles in the process of DNA replication, topoisomerases have been one of the major targets in the anticancer drug development area. A need, therefore, arises for new metallodrugs that specifically recognizes DNA and inhibits the activity of topoisomerase enzymes, herein, we report the synthesis and characterization of new metal-based glycoconjugate entities containing heterobimetallic core Cu^II-Sn^IV (1) and Ni^II-Sn^IV (2) derived from N-glycoside ligand (L). The optimized structure of complex 1 and other significant vibrational modes have been explained using dispersion corrected B3LYP/DFT calculations. In vitro DNA binding profile of the L and both the complexes 1 and 2 were done by various biophysical studies. Complex 1 breaks pBR322 DNA via a hydrolytic means which was validated by T4 DNA enzymatic assay. To get a mechanistic insight of mode of action topoisomerase I (Topo I) inhibition assay was carried out. Also, we have taken the help of molecular modeling studies in accordance with experimental findings. In vitro cytotoxicity of the complex 1 was evaluated against a panel of cancer cells which exhibited remarkably good anticancer activity (GI₅₀ values <10 μg/ml). Moreover, intracellular localization of the complex 1 was visualized by confocal microscopy against HeLa cells.

The development of ruthenium(ii) polypyridyl complexes and conjugates for in vitro cellular and in vivo applications

Ruthenium(ii) [Ru(ii)] polypyridyl complexes have been the focus of intense investigations since work began exploring their supramolecular interactions with DNA. In recent years, there have been considerable efforts to translate this solution-based research into a biological environment with the intention of developing new classes of probes, luminescent imaging agents, therapeutics and theranostics. In only 10 years the field has expanded with diverse applications for these complexes as imaging agents and promising candidates for therapeutics. In light of these efforts this review exclusively focuses on the developments of these complexes in biological systems, both in cells and in vivo, and hopes to communicate to readers the diversity of applications within which these complexes have found use, as well as new insights gained along the way and challenges that researchers in this field still face.

Single X-ray crystal structure, DFT studies and topoisomerase I inhibition activity of a tailored ionic Ag(i) nalidixic acid–piperazinium drug entity specific for pancreatic cancer cells

DFT studies, Topo I inhibition assay and cytotoxic activity of novel ionic Ag(i) nalidixic acid–piperazinium molecular entity.

Ruthenium(II) polypyridyl complexes with 1,8-naphthalimide group as DNA binder, photonuclease, and dual inhibitors of topoisomerases I and IIα

Two ruthenium(II) polypyridyl complexes containing 1,8-naphthalimide group as DNA binders, photonucleases, and inhibitors of topoisomerases I and IIα are evaluated. The binding properties of [Ru(phen)₂(pnip)]²⁺ {1; phen=1,10-phenanthroline; pnip=12-[N-(p-phenyl)-1,8-napthalimide]- imidazo[4',5'-f] [1,10]phenanthroline} and [Ru(bpy)₂(pnip)]²⁺ (2; bpy=2,2'-bipyridine) with calf thymus DNA increases with increasing the bulkiness and hydrophobic character of ancillary ligands, although the two complexes possess high affinities for DNA via intercalation. Moreover, photoirradiation (λ=365nm) of the two complexes are found to induce strand cleavage of closed circular pBR322 plasmid DNA via singlet oxygen mechanism, while complex 1 displays more effective photocleavage activity than complex 2 under the same conditions. Topoisomerase inhibition and DNA strand passage assay reflect that complexes 1 and 2 are efficient dual poisons of topoisomerases I and IIα.

Dual inhibition of topoisomerases I and IIα by ruthenium(II) complexes containing asymmetric tridentate ligands

Five novel ruthenium(II) complexes, [Ru(dtzp)(dppt)](2+) (1), [Ru(dtzp)(pti)](2+) (2), [Ru(dtzp)(ptn)](2+) (3), [Ru(dtzp)(pta)](2+) (4) and [Ru(dtzp)(ptp)](2+) (5) (where dtzp = 2,6-di(thiazol-2-yl)pyridine, dppt = 3-(1,10-phenanthroline-2-yl)-5,6-diphenyl-as-triazine), pti = 3-(1,10-phenanthroline-2-yl)-as-triazino-[5,6-f]isatin, ptn = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]naphthalene, pta = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]acenaphthylene, and ptp = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]-phenanthrene), were synthesised and characterised. The structures of complexes 3-5 were determined by X-ray diffraction. The DNA binding behaviours of the complexes were studied by spectroscopic and viscosity measurements. The results suggested that the Ru(II) complexes, except for complex 1, bind to DNA in an intercalative mode. Topoisomerase inhibition and DNA strand passage assay confirmed that Ru(II) complexes 3, 4, and 5 acted as efficient dual inhibitors of topoisomerases I and IIα. In vitro cytotoxicity assays indicated that these complexes exhibited anticancer activity against various cancer cell lines. Ruthenium(ii) complexes were confirmed to preferentially accumulate in the nucleus of cancer cells and induced DNA damage. Flow cytometric analysis and AO/EB staining assays indicated that these complexes induced cell apoptosis. With the loss of the mitochondrial membrane potential, the Ru(ii) complexes induce apoptosis via the mitochondrial pathway.

Interactions of octahedral ruthenium(II) polypyridyl complexes with the RNA triplex poly(U)•poly(A)*poly(U) effect on the third-strand stabilization

Stable triplexes play key roles in many biological processes. Due to the Hoogsteen base pairing, triplexes are, however, thermodynamically less stable than the corresponding duplexes. The poor stabilization of these structures limits their practical applications under physiological conditions. To understand the factors effect on the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the interactions of [RuL2(uip)](2+) {where L = 2,2'-bipyridine (bpy) or 1,10-phenanthroline phen, uip = 2-(5-uracil)-1H-imidazo[4,5-f][1,10]phenanthroline} with the RNA triplex poly(U)•poly(A)*poly(U) are examined by spectrophotometry, spectrofluorometry, circular dichroism, and viscosimetry in this work. The main results obtained here suggest that the third-strand stabilization depends on the hydrophobicity effects of ancillary ligands bpy and phen.

Chiral-auxiliary-mediated asymmetric synthesis of ruthenium polypyridyl complexes

An octahedral metal complex with 6 different monodentate ligands can form 15 diastereomers as pairs of enantiomers. As a result, the elaborate stereochemistry of octahedral coordination geometries provides tremendous opportunities in the fields of catalysis, the materials sciences, and the life sciences. The demand for enantiomerically pure coordination complexes for tasks related to the selective molecular recognition of biomacromolecules led us to develop synthetic methods to control the absolute stereochemistry at octahedral metal centers. A few years ago our laboratory therefore embarked on a project exploring new and general synthetic strategies for the asymmetric synthesis of inert octahedral transition metal complexes. We initially used the example of thermally inert ruthenium polypyridyl complexes and developed a family of chiral bidentate ligands, including salicyloxazolines, (mercaptophenyl)oxazolines, sulfinylphenols, N-acetylsulfinamides, a phosphinohydroxybinaphthyl, and even the amino acid proline to serve as chiral auxiliaries for asymmetric coordination chemistry. All these chiral auxiliaries strongly coordinate to ruthenium(II) in a bidentate, deprotonated fashion, allowing them to control the absolute metal-centered configuration in the course of subsequent ligand exchange reactions. Finally, we can remove them from the metal without any loss of chiral information and without leaving a chemical trace. A key feature of these chiral auxiliary ligands is their switchable binding strength. A chelate effect ensures that the chiral ligands coordinate very tightly to the metal center, placing their carbon-based, sulfur-based, or axial chirality in a well-defined position close to the metal center to efficiently establish the absolute metal-centered configuration. At the same time a coordinating phenolate, carboximidate, carboxylate, or thiophenolate moiety makes the coordination reversible by weakening the binding strength through protonation or methylation. Following this strategy, we synthesized a large number of homoleptic, bis-heteroleptic, and tris-heteroleptic ruthenium polypyridyl complexes in an asymmetric fashion with enantiomeric ratios that routinely reached or exceeded 96:4. Our approach should serve as a blueprint for the asymmetric synthesis of different classes of ruthenium complexes and chiral coordination complexes of other metals.

Dual topoisomerase I and II poisoning by chiral Ru(II) complexes containing 2-thiophenylimidazo[4,5-f][1,10]phenanthroline derivatives

A series of chiral Ru(II) complexes bearing thiophene ligands were synthesized and characterized. Both Ru(II) complexes Δ/Λ-[Ru(bpy)2(pscl)](2+) (Δ/Λ-1) and Δ/Λ-[Ru(bpy)2(psbr)](2+) (Δ/Λ-2) (bpy=2,2'-bipyridine, pscl=2-(5-chlorothiophen-2-yl)imidazo[4,5-f][1,10]phenanthroline, psbr=2-(5-bromothiophen-2-yl)imidazo[4,5-f][1,10]phenanthroline) showed antitumor activities against A549, HepG2 and BEL-7402 tumor cell lines, especially HeLa tumor cell line. Moreover, Δ enantiomers were more active than Λ enantiomers, accounting for the different cellular uptake. In addition, with the extension of time, these enantiomers could finally accumulate in the nucleus, suggesting that nucleic acids were the cellular target of these enantiomers. The DNA-binding behaviors of complexes were studied using spectroscopic and viscosity measurements. Results suggested that four complexes could bind to DNA in an intercalative mode but no obvious DNA-binding selectivity between the enantiomers was observed. Topoisomerase inhibition and DNA religation assay confirmed that four complexes acted as efficient dual topoisomerase I and II poisons, DNA strand breaks had also been observed from alkaline single cell gel electrophoresis (comet assay). Δ-1 and Δ-2 inhibited the growth of HeLa cells through the induction of apoptotic cell death, as evidenced by the Alexa Fluor® 488 annexin V staining assays and flow cytometry analysis. The results demonstrated that Δ/Λ-1 and Δ/Λ-2 acted as dual topoisomerase I and II poisons and caused DNA damage that could lead to cell cycle arrest by apoptosis.

Structure-activity relationship of polypyridyl ruthenium(II) complexes as DNA intercalators, DNA photocleavage reagents, and DNA topoisomerase and RNA polymerase inhibitors

To investigate the relationship between the molecular structure and biological activity of polypyridyl Ru(II) complexes, such as DNA binding, photocleavage ability, and DNA topoisomerase and RNA polymerase inhibition, six new [Ru(bpy)(2)(dppz)](2+) (bpy=2,2'-bipyridine; dppz=dipyrido[3,2-a:2,',3'-c]phenazine) analogs have been synthesized and characterized by means of (1)H-NMR spectroscopy, mass spectrometry, and elemental analysis. Interestingly, the biological properties of these complexes have been identified to be quite different via a series of experimental methods, such as spectral titration, DNA thermal denaturation, viscosity, and gel electrophoresis. To explain the experimental regularity and reveal the underlying mechanism of biological activity, the properties of energy levels and population of frontier molecular orbitals and excited-state transitions of these complexes have been studied by density-functional theory (DFT) and time-depended DFT (TDDFT) calculations. The results suggest that DNA intercalative ligands with better planarity, greater hydrophobicity, and less steric hindrance are beneficial to the DNA intercalation and enzymatic inhibition of their complexes.

Chiral ruthenium(II) complexes with phenolic hydroxyl groups as dual poisons of topoisomerases I and IIα

A series of novel chiral ruthenium(II) complexes with phenolic hydroxyl groups were synthesized and characterized. These ruthenium(II) complexes exhibited strong dual inhibition of topoisomerases I and IIα, with approximate IC50 values of 3-15 mM, which were more efficient than the widely clinically used single TopoI poison camptothecin (CPT) or TopoIIα poison etoposide (VP-16). Δ-1 and Λ-1 with more hydroxyls were observed to be more potent inhibitors. To further evaluate the mechanism of the complexes at a cellular level, these complexes were investigated for their effect on cell proliferation, cell cycle progression and induction of apoptosis. The results indicated that ruthenium(II) complexes permeated the nuclei in cancer cells and inhibited the activities of nuclear enzymes topoisomerases I and IIα, then triggered DNA damage and induced apoptosis in the cancer cells. The simultaneous inhibition of TopoI and TopoIIα induced the death of cancer cells, which may be a promising and effective strategy for cancer therapy.

Application of a europium complex, Eu(AA)3phen (AA=acrylic acid, phen=1,10-phenanthroline) as a spectroscopic probe and cleaving reagent of DNA

A complex Eu(AA)3phen was synthesized and characterized by elemental analysis, IR spectroscopy and (1)H NMR. Interaction between Eu(AA)3phen and DNA was studied by UV/visible absorption spectroscopy, fluorescence spectrophotometer, circular-dichroism (CD) spectra and gel-electrophoresis measurements. Absorption spectral indicated that Eu(AA)3phen binding to DNA was an electrostatic mode, which was authenticated by the effect of ionic strength, thermal denaturation and fluorescence quenching experiments. The intrinsic binding constant Kb of Eu(AA)3phen was calculated to be 1.6×10(4) L mol(-1).

Synthesis and Characterisation of RuII Polypyridyl Complexes: DNA-Binding, Photocleavage, and Topoisomerase I and II Inhibitory Activity

Two mixed-ligand ruthenium(ii) complexes [Ru(phen)2(cptcp)]2+ (Ru1; phen = 1,10-phenanthroline, cptcp = 2-(4-carbazol-9-yl-phenyl)-1H-1,3,7,8-tetraaza-cyclopenta-[l]-phenanthrene) and [Ru(phen)2(btcpc)]2+ (Ru2; btcpc = 9-butyl-6-(1H-1,3,7,8-tetraaza-cyclo-cyclopenta-[l]-phenanthren-2-yl)-9H-carbazole-3-carbaldehyde) have been synthesised and characterised. The DNA-binding behaviours of the two complexes have been investigated by using spectroscopic and viscosity measurements. Results suggest that the two complexes bind to DNA by intercalation. The photocleavage of plasmid pBR322 DNA indicates that Ru1 exhibits more effective DNA cleavage activity in comparison to that exhibited by Ru2 under the same conditions, and different cleavage mechanisms are determined. Topoisomerase inhibition and DNA strand passage assay confirm that Ru1 may act as an efficient dual inhibitor of topoisomerases I and II, whereas Ru2 may only act as a single inhibitor of topoisomerases II.

Theoretical studies on DNA-photocleavage efficiencies and mechanisms of Ru(II) polypyridyl complexes

Theoretical studies on the DNA-photocleavage efficiencies and mechanisms of Ru(II) complexes [Ru(bpy)(2)(L)](2+) (bpy = 2,2'-bipyridine; L: dppz = dipyrido[3,2-a:2',3'-c]phenazine; mitatp = 5-methoxy-isatino[1,2-b]-1,4,8,9-tetraazatriphenylene; nitatp = 5-nitro-isatino [1,2-b]-1,4,8,9-tetraazatriphenylene) 1-3 were carried out using density functional theory (DFT). First, the accuracies of redox potentials computed for [Ru(bpy)(3)](2+) in the ground state and the excited state by different computational methods were tested, and then the redox potentials of complexes 1-3 in their excited states were computed accurately. Secondly, the trend in the DNA-photocleavage efficiencies (ϕ) of complexes 1-3 [i.e., ϕ(2) > ϕ(3) > ϕ(1)] was reasonably well explained by their excited-state reduction potentials and their electron-transfer activation energies. Finally, the photoinduced oxidation-reduction mechanism utilized by these complexes was explored, and the DNA-photocleavage process was explained rationally.

New heterobimetallic Cu(II)-Sn2(IV) complex as potential topoisomerase I inhibitor: in vitro DNA binding, cleavage and cytotoxicity against human cancer cell lines

The new heterobimetallic Cu(II)-Sn(2)(IV)/Ni(II)-Sn(2)(IV) complexes 1 and 2 bearing bioactive pharmacophore ligand scaffold; 1,10-phenanthroline and ethylenediamine were synthesized and characterized by spectroscopic (IR, UV-vis, NMR, ESI-MS) and analytical methods. The in vitro DNA binding studies of 1 and 2 with CT-DNA were carried out by employing various biophysical methods which reveal strong electrostatic binding via phosphate backbone of DNA helix, in addition to partial intercalation in the minor groove and stabilized by intramolecular hydrogen bonding. To gain further insight into the molecular recognition at the target site, UV-vis titrations of 1 with 5'-GMP was carried out and validated by (1)H and (31)P NMR. Complex 1 cleaved pBR322 DNA via oxidative pathway and exhibited high inhibition activity against Topo-I at 20 μM. Furthermore, the cytotoxicity of 1 was examined on a panel of human tumor cell lines of different histological origins showing promising antitumor activity.