Insights into DNA Binding of Ruthenium Arene Complexes: Role of Hydrogen Bonding and π Stacking

"Half-Sandwich" Ruthenium Complexes with Alizarin as Anticancer Agents: In Vitro and In Vivo Studies

Upon exploration of the chemistry of the combination of ruthenium/arene with anthraquinone alizarin (L), three new complexes with the general formulas [Ru(L)Cl(η⁶-p-cymene)] (C1), [Ru(L)(η⁶-p-cymene)(PPh₃)]PF₆ (C2), and [Ru(L)(η⁶-p-cymene)(PEt₃)]PF₆ (C3) were synthesized and characterized using spectroscopic techniques (mass, IR, and 1D and 2D NMR), molar conductivity, elemental analysis, and X-ray diffraction. Complex C1 exhibited fluorescence, such as free alizarin, while in C2 and C3, the emission was probably quenched by monophosphines and the crystallographic data showed that hydrophobic interactions are predominant in intermolecular contacts. The cytotoxicity of the complexes was evaluated in the MDA-MB-231 (triple-negative breast cancer), MCF-7 (breast cancer), and A549 (lung) tumor cell lines and MCF-10A (breast) and MRC-5 (lung) nontumor cell lines. Complexes C1 and C2 were more selective to the breast tumor cell lines, and C2 was the most cytotoxic (IC₅₀ = 6.5 μM for MDA-MB-231). In addition, compound C1 performs a covalent interaction with DNA, while C2 and C3 present only weak interactions; however, internalization studies by flow cytometry and confocal microscopy showed that complex C1 does not accumulate in viable MDA-MB-231 cells and is detected in the cytoplasm only after cell permeabilization. Investigations of the mechanism of action of the complexes indicate that C2 promotes cell cycle arrest in the Sub-G₁ phase in MDA-MB-231, inhibits its colony formation, and has a possible antimetastatic action, impeding cell migration in the wound-healing experiment (13% of wound healing in 24 h). The in vivo toxicological experiments with zebrafish indicate that C1 and C3 exhibit the most zebrafish embryo developmental toxicity (inhibition of spontaneous movements and heartbeats), while C2, the most promising anticancer drug in the in vitro preclinical tests, revealed the lowest toxicity in in vivo preclinical screening.

Interaction of an anticancer benzopyrane derivative with DNA: Biophysical, biochemical, and molecular modeling studies

BACKGROUND

SIMR1281 is a potent anticancer lead candidate with multi- target activity against several proteins; however, its mechanism of action at the molecular level is not fully understood. Revealing the mechanism and the origin of multitarget activity is important for the rational identification and optimization of multitarget drugs.

METHODS

We have used a variety of biophysical (circular dichroism, isothermal titration calorimetry, viscosity, and UV DNA melting), biochemical (topoisomerase I & II assays) and computational (molecular docking and MD simulations) methods to study the interaction of SIMR1281 with duplex DNA structures.

RESULTS

The biophysical results revealed that SIMR1281 binds to dsDNA via an intercalation-binding mode with an average binding constant of 3.1 × 10⁶ M^-1. This binding mode was confirmed by the topoisomerases' inhibition assays and molecular modeling simulations, which showed the intercalation of the benzopyrane moiety between DNA base pairs, while the remaining moieties (thiazole and phenyl rings) sit in the minor groove and interact with the flanking base pairs adjacent to the intercalation site.

CONCLUSIONS

The DNA binding characteristics of SIMR1281, which can disrupt/inhibit DNA function as confirmed by the topoisomerases' inhibition assays, indicate that the observed multi-target activity might originate from ligand intervention at nucleic acids level rather than due to direct interactions with multiple biological targets at the protein level.

GENERAL SIGNIFICANCE

The findings of this study could be helpful to guide future optimization of benzopyrane-based ligands for therapeutic purposes.

Mo(VI) Potential Metallodrugs: Explaining the Transport and Cytotoxicity by Chemical Transformations

The transport and cytotoxicity of molybdenum-based drugs have been explained with the concept of chemical transformation, a very important idea in inorganic medicinal chemistry that is often overlooked in the interpretation of the biological activity of metal-containing systems. Two monomeric, [MoO₂(L¹)(MeOH)] (1) and [MoO₂(L²)(EtOH)] (2), and two mixed-ligand dimeric Mo^VIO₂ species, [{MoO₂(L^1-2)}₂(μ-4,4'-bipy)] (3-4), were synthesized and characterized. The structures of the solid complexes were solved through SC-XRD, while their transformation in water was clarified by UV-vis, ESI-MS, and DFT. In aqueous solution, 1-4 lead to the penta-coordinated [MoO₂(L^1-2)] active species after the release of the solvent molecule (1 and 2) or removal of the 4,4'-bipy bridge (3 and 4). [MoO₂(L^1-2)] are stable in solution and react with neither serum bioligand nor cellular reductants. The binding affinity of 1-4 toward HSA and DNA were evaluated through analytical and computational methods and in both cases a non-covalent interaction is expected. Furthermore, the in vitro cytotoxicity of the complexes was also determined and flow cytometry analysis showed the apoptotic death of the cancer cells. Interestingly, μ-4,4'-bipy bridged complexes 3 and 4 were found to be more active than monomeric 1 and 2, due to the mixture of species generated, that is [MoO₂(L^1-2)] and the cytotoxic 4,4'-bipy released after their dissociation. Since in the cytosol neither the reduction of Mo^VI to Mo^V/IV takes place nor the production of reactive oxygen species (ROS) through Fenton-like reactions of 1-4 with H₂O₂ occurs, the mechanism of cytotoxicity should be attributable to the direct interaction with DNA that happens with a minor-groove binding which results in cell death through an apoptotic mechanism.

meso-Tetra-(4-pyridyl)porphyrin/palladium(II) complexes as anticancer agents

This study reports the synthesis, structural characterization and cytotoxic activity of four new palladium/pyridylporphyrin complexes, with the general formula {TPyP[PdCl(P-P)]₄}(PF₆)₄, where P-P is 1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)butane (dppb) or 1,1'-bis(diphenylphosphino)ferrocene (dppf). The complexes were characterized by elemental analysis, and by FT-IR, UV/Vis, ¹H and ³¹P{¹H} NMR (1D/2D) spectroscopy. The slow evaporation of a methanolic solution of {TPyP[PdCl(dppb)]₄}(PF₆)₄ (in an excess of NaBF₄ salt) resulted in single crystals suitable for X ray diffraction, allowing the determination of the tridimensional structure of this complex, which crystallized in the P2₁/a space group. The cytotoxicity of the complexes against MDA-MB-231 (breast cancer cells) and MCF-10A (non-tumor breast cancer cells), was determined by the colorimetric MTT method, which revealed that all four complexes show selective indexes close to 1.2, lower than that of cisplatin for the same cells (12.12). The interaction of the complexes with CT-DNA was evaluated by UV-visible and viscosity measurements and it was determined that the complexes interact moderately with CT-DNA, probably by H-bonding/π-π stacking and electrostatic interactions.

Ruthenium(II) Complexes as Potential Apoptosis Inducers in Cancer Therapy

The compound cis-diamminedichloroplatinum(II) (cisplatin) is the most widely used anticancer drug, but due to its serious side effects (including gastrointestinal symptoms, renal tubular injury, neuromuscular complications, and ototoxicity), clinical applications of cisplatin are limited. Therefore, these limitations have provided an encouragement for further research into other transition metal complexes, with an aim to overcome the disadvantages related with cisplatin therapy. In the search for effective complexes that can be targeted against tumor cells, many research groups synthesized various ruthenium( II) complexes with different ligands. Also, newly synthesized ruthenium(II) complexes showed selective anticancer activity against different types of cancer cells. Activity of ruthenium(II) complexes in some cases was even higher than that of cisplatin against the same cells. Precise mechanism of action of ruthenium(II) complexes is not fully understood. The different examples mentioned in this review showed that ruthenium(II) complexes decreased viability of cancer cells by induction of apoptosis and/or by cell cycle arrest which implies their different mechanism of action against different types of cancer cells.

Anticancer and antimicrobial properties of novel η6-p-cymene ruthenium(ii) complexes containing a N,S-type ligand, their structural and theoretical characterization

Ruthenium(ii) complexes are lately of great scientific interest due to their chemotherapeutic potential as anticancer and antimicrobial agents. Here we present the synthesis of new pyrazole carbothioamide derivatives and their four arene–ruthenium complexes. The title compounds were characterized with the application of IR, NMR, mass spectrometry, elemental analysis and X-ray diffraction. Additionally, for new complexes DFT calculations were done. Their antimicrobial activity (MIC, MBC/MFC) was examined in vitro against Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, Proteus vulgaris and Candida albicans. Their cytotoxic effects, using the MTT assay, against three cancer cell lines: HL-60, NALM-6, WM-115 and normal human foreskin fibroblasts (HFF-1) were also investigated. The influence of the new arene–ruthenium(ii) complexes on the DNA structure was also tested. From our results, compound 2d showed higher cytotoxicity against melanoma cell line WM-115 than cisplatin. Strong biostatic and biocidal activity of the tested complexes against Gram-positive bacteria, including S. aureus, S. epidermidis and E. faecalis was demonstrated. The new arene–ruthenium(ii) compounds could not only inhibit proliferation of cancer cells, but also protect patients against malignant wound infections.

New arene–ruthenium(ii) complexes with pyrazole derivatives as ligands were synthesized and characterized. This compounds exhibited good cytotoxic effects, and strong biostatic and biocidal activity.

Competition Between π-π and C-H/π Interactions: A Comparison of the Structural and Electronic Properties of Alkoxy-Substituted 1,8-Bis((propyloxyphenyl)ethynyl)naphthalenes

The structural and electronic consequences of π-π and C-H/π interactions in two alkoxy-substituted 1,8-bis- ((propyloxyphenyl)ethynyl)naphthalenes are explored by using X-ray crystallography and electronic structure computations. The crystal structure of analogue 4, bearing an alkoxy side chain in the 4-position of each of the phenyl rings, adopts a π-stacked geometry, whereas analogue 8, bearing alkoxy groups at both the 2- and the 5-positions of each ring, has a geometry in which the rings are splayed away from a π-stacked arrangement. Symmetry-adapted perturbation theory analysis was performed on the two analogues to evaluate the interactions between the phenylethynyl arms in each molecule in terms of electrostatic, steric, polarization, and London dispersion components. The computations support the expectation that the π-stacked geometry of the alkoxyphenyl units in 4 is simply a consequence of maximizing π-π interactions. However, the splayed geometry of 8 results from a more subtle competition between different noncovalent interactions: this geometry provides a favorable anti-alignment of C-O bond dipoles, and two C-H/π interactions in which hydrogen atoms of the alkyl side chains interact favorably with the π electrons of the other phenyl ring. These favorable interactions overcome competing π-π interactions to give rise to a geometry in which the phenylethynyl substituents are in an offset, unstacked arrangement.

A comparative DFT study on aquation and nucleobase binding of ruthenium (II) and osmium (II) arene complexes

The potential energy surfaces of the reactions of organometallic arene complexes of the type [(η (6)-arene)M(II)(pic)Cl] (where pic = 2-picolinic acid, M = Ru or Os) were examined by a DFT computational study. Among the seven density functional methods, hybrid exchange functional B3LYP outperforms the others to explain the aquation of the complexes. The reactions and binding energies of Ru(II) and Os(II) arene complexes with both 9EtG and 9EtA were studied to gain insight into the reactivity of these types of organometallic complexes with DNA. The obtained data rationalize experimental observation, contributing to partly understanding the potential biological and medical applications of organometallic complexes.

Competition between glutathione and DNA oligonucleotides for ruthenium(II) arene anticancer complexes

The organometallic anticancer complex [(η(6)-bip)Ru(en)Cl](+) (1; bip = biphenyl, en = ethylenediamine) selectively binds to N7 of guanine bases of oligonucleotides and native DNA. However, under physiologically relevant conditions (micromolar Ru concentrations, pH 7, 22 mM NaCl, 310 K), the tripeptide glutathione (γ-L-Glu-L-Cys-Gly; GSH) is kinetically competitive with guanine (as guanosine 3',5'-cyclic monophosphate, cGMP) for coordination with complex 1, and gives rise to a ruthenium thiolato adduct. This thiolato adduct can subsequently undergo oxidation to a sulfenate intermediate, providing a facile route for the formation of a final cGMP adduct via the displacement of S-bound glutathione by G N7 (F. Y. Wang, J. J. Xu, A. Habtemariam, J. Bella and P. J. Sadler, J. Am. Chem. Soc., 2005, 127, 17734). In this work, the competition between GSH and the single-stranded 14-mer oligonucleotide 5'-TATGTACCATGTAT-3' (I) and duplex III (III = I + II, II = 5'-ATACATGGTACATA) for complex 1 and its analogue [(η(6)-tha)Ru(en)Cl](+) (2, tha = tetrahydroanthracene) under physiologically relevant conditions was investigated using conventional ESI-MS and high resolution ESI-FTICR-MS coupled to conventional HPLC and nanoscale HPLC, respectively. The results indicate that whether there was high excess of GSH or not in the reaction mixtures, the reaction of complex 1 or 2 with single-stranded oligonucleotide I always gave rise to mono-ruthenated oligonucleotide, and the reaction of complex 1 or 2 with duplex III gave rise to the mono-ruthenated duplex oligonucleotide. Furthermore, the ruthenation of duplex III by complex 1 showed no significant discrimination between the complementary strands I and II, but complex 2 appeared to bind preferentially to strand II compared to strand I as revealed by the high resolution FTICR-MS analysis. GSH is highly abundant in cells at millimolar concentrations and is well known to be involved in the deactivation of the clinical drug cisplatin and in platinum resistance. Our findings reveal a potentially contrasting role for GSH in the mechanism of action of these ruthenium anticancer complexes that may contribute to the lack of cross-resistance with platinum drugs.

Photodissociation of a ruthenium(II) arene complex and its subsequent interactions with biomolecules: a density functional theory study

The piano-stool Ru(II) arene complex [(η⁶-benz)Ru(bpm)(py)]²⁺ (benz = benzene, bpm = 2,2'-bipyrimidine, and py = pyridine), which is conventionally nonlabile (on a timescale and under conditions relevant for biological reactivity), can be activated by visible light to selectively photodissociate the monodentate ligand (py). In the present study, the aquation and binding of the photocontrolled ruthenium(II) arene complex [(η⁶-benz)Ru(bpm)(py)]²⁺ to various biomolecules are studied by density functional theory (DFT) and time-dependent DFT (TDDFT). Potential energy curves (PECs) calculated for the Ru-N (py) bonds in [(η⁶-benz)Ru(bpm)(py)]²⁺ in the singlet and triplet state give useful insights into the photodissociation mechanism of py. The binding energies of the various biomolecules are calculated, which allows the order of binding affinities among the considered nuleic-acid- or protein-binding sites to be discerned. The kinetics for the replacement of water in the aqua complex with biomolecules is also considered, and the results demonstrate that guanine is superior to other biomolecules in terms of coordinating with the Ru(II) aqua adduct, which is in reasonable agreement with experimental observations.

Decameric uracil complexes around Li+

Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings.

Encapsulation of ruthenium nitrosylnitrate and DNA purines in nanostructured sol-gel silica matrices

The interactions between DNA purines (guanine and adenine) and the ruthenium complex Ru(NO)(NO(3))(3) were studied within nanostructured silica matrices prepared by a two-step sol-gel process. By infrared analysis in diffuse reflectance mode, it was proved that encapsulation induces a profound modification on the complex, whereas guanine and adenine preserve their structural integrity. The complex undergoes nitrate ligand exchange and co-condenses with the silica oligomers, but the nitrosyl groups remain stable, which is an unusual behavior in Ru nitrosyl complexes. In turn, the doping molecules affect the sol-gel reactions and eventually the silica structure as it forms: the complex yields a microporous structure, and the purine bases are responsible for the creation of macropores due to hydrogen bonding with the silanol groups of the matrix. In a confined environment, the interactions are much stronger for the coencapsulated pair guanine complex. While adenine only establishes hydrogen bonds or van der Waals interactions with the complex, guanine bonds covalently to Ru by one N atom of the imidazole ring, which becomes strongly perturbed, resulting in a deformation of the complex geometry.