DNA interactions of monofunctional organometallic ruthenium(II) antitumor complexes in cell-free media

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.

DNA binding and cytotoxicity of ruthenium(II) and rhenium(I) complexes of 2-amino-4-phenylamino-6-(2-pyridyl)-1,3,5-triazine

[Ru(tBu2bpy)2(2-appt)](PF6)2 [1.(PF6)2, tBu2bpy = 4,4'-di-tert-butyl-2,2'-bipyridine, 2-appt = 2-amino-4-phenylamino-6-(2-pyridyl)-1,3,5-triazine] and [Re(CO)3(2-appt)Cl] (2) were prepared and characterized by X-ray crystal analysis. The binding of 1.(PF6)2 and 2 to calf thymus DNA (ct DNA) led to increases in the DNA melting temperature (Delta Tm = +12 degrees C), modest hypochromism (29% and 5% of the absorption bands at lambda max = 450 and 376 nm, respectively), and insignificant shifts in the absorption maxima. The binding constants of 1.(PF6)2 and 2 with ct DNA, as determined by absorption titration, are (8.9 +/- 0.5) x 104 and (3.6 +/- 0.1) x 104 dm3 mol-1, respectively. UV-vis absorption titration, DNA melting studies, and competition dialysis using synthetic oligonucleotides [poly(dA-dT)2 and poly(dG-dC)2] revealed that 1.(PF6)2 and 2 exhibit a binding preference for AT sequences. A modeling study on the interaction between 1 or 2 and B-DNA revealed that the minor groove is the most favored binding site and an extensive hydrogen-bonding network is formed. As determined by MTT assays, 1.(PF6)2 and 2 exhibited moderate cytotoxicities toward several human cancer cell lines (KB-3-1, HepG2, and HeLa), as well as a multi-drug-resistant cancer cell line (KB-V-1). According to confocal microscopic and flow cytometric studies, 1.(PF6)2 and 2 induced apoptosis (50-60%) in cancer cells with <5% necrosis detected.

Synthesis, characterization, antibacterial activity, and interaction with DNA of the vanadyl-enrofloxacin complex

The neutral mononuclear vanadyl complex with the quinolone antibacterial drug enrofloxacin has been prepared and characterized with physicochemical and spectroscopic techniques and molecular mechanics calculations. The interaction of the complex with calf-thymus DNA has also been investigated and the antimicrobial activity has been evaluated against three different microorganisms.

Ruthenium complexes can target determinants of tumour malignancy

Metastases are more decisive for tumour prognosis than primary lesions, because of their multiple locations, low accessibility to surgery and/or radiotherapy, and generally poor responsiveness to chemotherapy. The metastasis should therefore be the primary target for drug therapy. Among ruthenium complexes, NAMI-A is a leading compound that shows selective effects for solid tumour metastases related to a mechanism of action involving the inhibition of the processes of tumour invasiveness. NAMI-A opens an avenue to new perspectives in cancer chemotherapy. This includes novel compounds directed at targets selectively expressed by tumour metastases, thus reducing the typical side effects of the current metal-based drugs that are active via their unselective DNA interaction.

Phenylazo-pyridine and phenylazo-pyrazole chlorido ruthenium(II) arene complexes: arene loss, aquation, and cancer cell cytotoxicity

Ru(II) eta6-arene complexes containing p-cymene (p-cym), tetrahydronaphthalene (thn), benzene (bz), or biphenyl (bip), as the arene, phenylazopyridine derivatives (C5H4NN:NC6H5R; R = H (azpy), OH (azpy-OH), NMe2 (azpy-NMe2)) or a phenylazopyrazole derivative (NHC3H2NN:NC6H5NMe2 (azpyz-NMe2)) as N,N-chelating ligands and chloride as a ligand have been synthesized (1-16). The complexes are all intensely colored due to metal-to-ligand charge-transfer Ru 4d6-pi* and intraligand pi -->pi* transitions (eta = 5000-63 700 M-1 cm-1) occurring in the visible region. In the crystal structures of [(eta6-p-cym)Ru(azpy)Cl]PF6 (1), [(eta6-p-cym)Ru(azpy-NMe2)Cl]PF6 (5), and [(eta6-bip)Ru(azpy)Cl]PF6 (4), the relatively long Ru-N(azo) and Ru-(arene-centroid) distances suggest that phenylazopyridine and arene ligands can act as competitive pi-acceptors toward Ru(II) 4d6 electrons. The pKa* values of the pyridine nitrogens of the ligands are low (azpy 2.47, azpy-OH 3.06 and azpy-NMe2 4.60), suggesting that they are weak sigma-donors. This, together with their pi-acceptor behavior, serves to increase the positive charge on ruthenium, and together with the pi-acidic eta6-arene, partially accounts for the slow decomposition of the complexes via hydrolysis and/or arene loss (t(1/2) = 9-21 h for azopyridine complexes, 310 K). The pKa* of the coordinated water in [(eta6-p-cym)Ru(azpyz-NMe2)OH2]2+ (13A) is 4.60, consistent with the increased acidity of the ruthenium center upon coordination to the azo ligand. None of the azpy complexes were cytotoxic toward A2780 human ovarian or A549 human lung cancer cells, but several of the azpy-NMe2, azpy-OH, and azpyz-NMe2 complexes were active (IC50 values 18-88 microM).

Ruthenation of duplex and single-stranded d(CGGCCG) by organometallic anticancer complexes

We have studied the interaction of the organometallic anticancer ruthenium(II) complexes [(eta(6)-p-cymene)Ru(en)Cl][PF(6)] (1) and [(eta(6)-biphenyl)Ru(en)Cl][PF(6)] (2) (en=ethylenediamine) with the single-stranded (ss) DNA hexamer d(CGGCCG) (I) and the duplex d(CGGCCG)(2) (II) by HPLC, ESI-MS, and one- and two-dimensional (1)H and (15)N NMR spectroscopy. For ss-DNA, all three G's are readily ruthenated with [(eta(6)-arene)Ru(en)](2+), but for duplex DNA there is preferential ruthenation of G3 and G6, and no binding to G2 was detected. For monoruthenated duplexes, N7 ruthenation of G is accompanied by strong hydrogen bonding between G-O6 and en-NH for the p-cymene adducts. Intercalation of the non-coordinated phenyl ring between G3 and C4 or G6 and C5 was detected in the biphenyl adducts of mono- and diruthenated duplexes, together with weakening of the G-O6NH-en hydrogen bonding. The arene ligand plays a major role in distorting the duplex either through steric interactions (p-cymene) or through intercalation (biphenyl).

Structure-activity relationships for cytotoxic ruthenium(II) arene complexes containing N,N-, N,O-, and O,O-chelating ligands

We report structure-activity relationships for organometallic RuII complexes of the type [(eta6-arene)Ru(XY)Cl]Z, where XY is an N,N- (diamine), N,O- (e.g., amino acidate), or O,O- (e.g., beta-diketonate) chelating ligand, the arene ranges from benzene derivatives to fused polycyclic hydrocarbons, and Z is usually PF6. The X-ray structures of 13 complexes are reported. All have the characteristic "piano-stool" geometry. The complexes most active toward A2780 human ovarian cancer cells contained XY=ethylenediamine (en) and extended polycyclic arenes. Complexes with polar substituents on the arene or XY=bipyridyl derivatives exhibited reduced activity. The activity of the O,O-chelated complexes depended strongly on the substituents and on the arene. For arene=p-cymene, XY=amino acidate complexes were inactive. Complexes were not cross-resistant with cisplatin, and cross-resistance to Adriamycin was circumvented by replacing XY=en with 1,2-phenylenediamine. Some complexes were also active against colon, pancreatic, and lung cancer cells.

Crystal structure, spectroscopic, and biological study of the copper(II) complex with third-generation quinolone antibiotic sparfloxacin

The neutral mononuclear copper(II) complex with the quinolone antibacterial drug sparfloxacin has been prepared and characterized with IR, UV-vis, and EPR spectroscopies and X-ray crystallography. The interaction of the complex with calf-thymus DNA has also been investigated and the antimicrobial activity has been evaluated against three different microorganisms.

Neutral and cationic mononuclear copper(II) complexes with enrofloxacin: structure and biological activity

The mononuclear copper complexes with the quinolone antibacterial drug enrofloxacin (=Herx) in the presence or not of a nitrogen donor heterocyclic ligand 1,10-phenanthroline (=phen) and 2,2'-bipyridine (=bipy) have been prepared and characterized. Interaction of copper(II) with deprotonated enrofloxacin leads to the formation of the neutral complex Cu(erx)2(H2O), 1, while the presence of phen or bipy leads to the formation of a neutral or a cationic mononuclear complex, respectively. The crystal structures of (chloro)(1,10-phenanthroline)(enrofloxacinato)copper(II), 2, and (aqua)(2,2'-bipyridine)(enrofloxacinato)copper(II) chloride, 3, have been determined with X-ray crystallography. The complexes have been studied with X-band electron paramagnetic resonance in aqueous solutions at liquid helium temperature. The study of the interaction of the complexes with calf-thymus DNA has been performed with diverse spectroscopic techniques and has showed that all complexes are bound to DNA by the intercalative mode. The antimicrobial efficiency of the complexes has been tested on three different microorganisms and the available evidence supports that the best inhibition is provided by Cu(erx)2(H2O) (minimum inhibitory concentration=0.125 microg mL(-1)) against Escherichia coli and Pseudomonas aeruginosa.

Competition between glutathione and guanine for a ruthenium(II) arene anticancer complex: detection of a sulfenato intermediate

The organometallic anticancer complex [(eta6-bip)Ru(en)Cl]+ (1; bip = biphenyl, en = ethylenediamine) selectively binds to guanine (N7) bases of DNA (Novakova, O.; Chen, H.; Vrana, O.; Rodger, A.; Sadler, P. J.; Brabec, V. Biochemistry 2003, 42, 11544-11554). In this work, competition between the tripeptide glutathione (gamma-L-Glu-L-Cys-Gly; GSH) and guanine (as guanosine 3',5'-cyclic monophosphate, cGMP) for complex 1 was investigated using HPLC, LC-MS and 1H,15N NMR spectroscopy. In unbuffered solution (pH ca. 3), the reaction of 1 with GSH gave rise to three intermediates: an S-bound thiolato adduct [(eta6-bip)Ru(en)(GS-S)] (4) and two carboxylate-bound glutathione products [(eta6-bip)Ru(en)(GSH-O)]+ (5, 6) during the early stages (<6 h), followed by en displacement and formation of a tri-GS-bridged dinuclear Ru(II) complex [((eta6-bip)Ru)2(GS-mu-S)3]2- (7). Under physiologically relevant conditions (micromolar Ru concentrations, pH 7, 22 mM NaCl, 310 K), the thiolato complex 4 was unexpectedly readily oxidized by dioxygen to the sulfenato complex [(eta6-bip)Ru(en)(GS(O)-S)] (8) instead of forming the dinuclear complex 7. Under these conditions, competitive reaction of complex 1 with GSH and cGMP gave rise to the cGMP adduct [(eta6-bip)Ru(en)(cGMP-N7)]+ (10) as the major product, accounting for ca. 62% of total Ru after 72 h, even in the presence of a 250-fold molar excess of GSH. The oxidation of coordinated glutathione in the thiolato complex 4 to the sulfenate in 8 appears to provide a facile route for displacement of S-bound glutathione by G N7. Redox reactions of cysteinyl adducts of these Ru(II) arene anticancer complexes could therefore play a significant role in their biological activity.

Controlling ligand substitution reactions of organometallic complexes: tuning cancer cell cytotoxicity

Organometallic compounds offer broad scope for the design of therapeutic agents, but this avenue has yet to be widely explored. A key concept in the design of anticancer complexes is optimization of chemical reactivity to allow facile attack on the target site (e.g., DNA) yet avoid attack on other sites associated with unwanted side effects. Here, we consider how this result can be achieved for monofunctional "piano-stool" ruthenium(II) arene complexes of the type [(eta6-arene)Ru(ethylenediamine)(X)]n+. A potentially important activation mechanism for reactions with biomolecules is hydrolysis. Density functional calculations suggested that aquation (substitution of X by H2O) occurs by means of a concerted ligand interchange mechanism. We studied the kinetics and equilibria for hydrolysis of 21 complexes, containing, as X, halides and pseudohalides, pyridine (py) derivatives, and a thiolate, together with benzene (bz) or a substituted bz as arene, using UV-visible spectroscopy, HPLC, and electrospray MS. The x-ray structures of six complexes are reported. In general, complexes that hydrolyze either rapidly {e.g., X = halide [arene = hexamethylbenzene (hmb)]} or moderately slowly [e.g., X = azide, dichloropyridine (arene = hmb)] are active toward A2780 human ovarian cancer cells, whereas complexes that do not aquate (e.g., X = py) are inactive. An intriguing exception is the X = thiophenolate complex, which undergoes little hydrolysis and appears to be activated by a different mechanism. The ability to tune the chemical reactivity of this class of organometallic ruthenium arene compounds should be useful in optimizing their design as anticancer agents.

Guanine and plasmid DNA binding of mono- and trinuclear fac-[Re(CO)3]+ complexes with amino acid ligands

We have synthesized and fully characterized four new complexes comprising the fac-[Re(CO)3]+ moiety and the ligands NH3, L-proline (Pro), or N,N-dimethylglycine (dmGly). The reaction of [Re(H2O)3(CO)3]+ with the two amino acids gives trinuclear complexes of general formula [Re(L)(CO)3]3 (where L = amino acid). We have studied the in vitro behavior of these compounds with guanine and DNA in order to understand whether the cytotoxicity exhibited by certain rhenium complexes based on the fac-[Re(CO)3]+ core is due to the formation of nucleobase complexes and inter- or intrastrand links between DNA bases. We have performed model studies with guanine and studied the structural effects induced by different rhenium(I) tricarbonyl complexes on PhiX174 plasmid DNA by electrophoretic methods. Our results show that rhenium complexes with two available coordination sites interact with plasmid DNA to form a stable adduct that is likely to involve two bases.

Organometallic chemistry, biology and medicine: ruthenium arene anticancer complexes

Our work has shown that certain ruthenium(II) arene complexes exhibit promising anticancer activity in vitro and in vivo. The complexes are stable and water-soluble, and their frameworks provide considerable scope for optimising the design, both in terms of their biological activity and for minimising side-effects by variations in the arene and the other coordinated ligands. Initial studies on amino acids and nucleotides suggest that kinetic and thermodynamic control over a wide spectrum of reactions of Ru(II) arene complexes with biomolecules can be achieved. These Ru(II) arene complexes appear to have an altered profile of biological activity in comparison with metal-based anticancer complexes currently in clinical use or on clinical trial.

Biophysical studies of a ruthenium(II) polypyridyl complex binding to DNA and RNA prove that nucleic acid structure has significant effects on binding behaviors

The interactions of a metal complex [Ru(phen)(2)PMIP](2+) {Ru=ruthenium, phen=1,10-phenanthroline, PMIP=2-(4-methylphenyl)imidazo[4,5-f]1,10-phenanthroline} with yeast tRNA and calf thymus DNA (CT DNA) have been investigated comparatively by UV-vis spectroscopy, fluorescence spectroscopy, viscosity measurements, isothermal titration calorimetry (ITC), as well as equilibrium dialysis and circular dichroism (CD). Spectroscopic studies together with ITC and viscosity measurements indicate that both binding modes of the Ru(II) polypyridyl complex to yeast tRNA and CT DNA are intercalation and yeast tRNA binding of the complex is stronger than CT DNA binding. ITC experiments show that the interaction of the complex with yeast tRNA is driven by a moderately favorable enthalpy decrease in combination with a moderately favorable entropy increase, while the binding of the complex to CT DNA is driven by a large favorable enthalpy decrease with a less favorable entropy increase. The results from equilibrium dialysis and CD suggest that both interactions are enantioselective and the Delta enantiomer of the complex may bind more favorably to both yeast tRNA and CT DNA than the Lambda enantiomer does, and that the complex is a better candidate for an enantioselective binder to yeast tRNA than to CT DNA. Taken together, these results indicate that the structures of nucleic acids have significant effects on the binding behaviors of metal complexes.

Metal complex-DNA interactions: from transcription inhibition to photoactivated cleavage

Metal ions and complexes, because of their cationic character, three-dimensional structural profiles, and propensity for performing hydrolysis, redox, or photoreactions, have a natural aptitude for interacting with DNA. Indeed, the need for cellular regulation of DNA led to the evolution of metallonucleases to catalyze and repair DNA strand breaks. Moreover, inorganic constructs such as cisplatin and bimetallic rhodium acetate exert antitumor activity by inner-sphere coordination to DNA. Because binding and cleavage of DNA is at the heart of cellular transcription and translation, it is an obvious target for therapeutic intervention and the development of diagnostic structural probes. To this end, new metal complexes have been designed that utilize or create open coordination positions for DNA binding and hydrolysis, generate reactive oxygen-containing species or other radicals for DNA oxidation, or perform direct redox reactions with DNA. The recent emerging themes are the development of bifunctional architectures containing multiple metal-binding or reactive sites, specialized ligand implementation, or incorporation of site-specific targeting substructures. This review describes their employment in novel reaction strategies that do not require bimolecular cofactors and as site-specific probes or cleavage agents.

Investigation of the role of Bax, p21/Waf1 and p53 as determinants of cellular responses in HCT116 colorectal cancer cells exposed to the novel cytotoxic ruthenium(II) organometallic agent, RM175

Ruthenium(II) organometallic complexes form monofunctional adducts with guanine in DNA in vitro and have a cytotoxic anticancer activity spectrum in preclinical models suggesting lack of cross-resistance with cisplatin. The primary cytotoxic lesion remains to be identified but the downstream mechanism of action is nevertheless of interest. Using isogenic derivatives of the HCT116 colorectal cancer cell line, we investigated the role of p53, p21/WAF1 and Bax in the cellular response to the novel ruthenium(II) organometallic complex RM175, [(eta(6)-C(6)H(5)C(6)H(5))RuCl (H(2)NCH(2)CH(2)NH(2)-N,N')](+) PF(6)(-). Western blotting demonstrated dose-dependent accumulation of p53, Bax and p21/WAF1 within 48 h of the start of RM175 treatment in wild-type HCT116 cells. HCT116 wild-type and Bax-null cells arrested in the G(1) and G(2) phases of the cell cycle. This pattern of cell cycle arrest was not observed in p53-null or in p21/WAF1-null cells. Following RM175 treatment, HCT116 wild-type and p21/WAF1 null cells underwent a dose-dependent induction of apoptosis (Annexin-V and sub-G(1) apoptosis assays). This apoptotic response was not observed in p53-null or Bax-null cells. In short-term sulphorhodamine B assays, the IC(50) for RM175 was 16 microM for p53-null HCT116, and 8 microM for wild-type cells (P<0.05). However, the sensitivity to RM175 in clonogenic assays at 16 days was independent of p53 status. These results identify determinants of the short-term in vitro response to RM175 demonstrating a role for p53 and p21/WAF1 in the growth arrest and for p53 and Bax in the apoptotic response. The mechanism of p53-independent suppression of long-term clonogenicity remains to be determined.

Conformation of DNA Modified by Monofunctional Ru(II) Arene Complexes: Recognition by DNA Binding Proteins and Repair. Relationship to Cytotoxicity

We analyzed DNA duplexes modified at central guanine residues by monofunctional Ru(II) arene complexes [(eta(6)-arene)Ru(II)(en)(Cl)](+) (arene = tetrahydroanthracene or p-cymene, Ru-THA or Ru-CYM, respectively). These two complexes were chosen as representatives of two different classes of Ru(II) arene compounds for which initial studies revealed different binding modes: one that may involve DNA intercalation (tricyclic-ring Ru-THA) and the other (mono-ring Ru-CYM) that may not. Ru-THA is approximately 20 times more toxic to cancer cells than Ru-CYM. The adducts of Ru-THA and Ru-CYM have contrasting effects on the conformation, thermodynamic stability, and polymerization of DNA in vitro. In addition, the adducts of Ru-CYM are removed from DNA more efficiently than those of Ru-THA. Interestingly, the mammalian nucleotide excision repair system has low efficiency for excision of ruthenium adducts compared to cisplatin intrastrand crosslinks.

Induced-fit recognition of DNA by organometallic complexes with dynamic stereogenic centers

Organometallic chemistry offers novel concepts in structural diversity and molecular recognition that can be used in drug design. Here, we consider DNA recognition by eta 6-arene Ru(II) anticancer complexes by an induced-fit mechanism. The stereochemistry of the dinuclear complex [((eta 6-biphenyl)RuCl(en))2-(CH2)6]2 + (3, en = ethylenediamine) was elucidated by studies of the half unit [(eta 6-biphenyl)RuCl(Et-en)]+ (2, where Et-en is Et(H)NCH2CH2NH2). The structures of the separated RRu*RN* and SRu*RN* diastereomers of 2 were determined by x-ray crystallography; their slow interconversion in water (t(1/2) approximately 2 h, 298 K, pH 6.2) was observed by NMR spectroscopy. For 2 and 3 the RRu*RN* configurations are more stable than SRu*RN* (73:27). X-ray and NMR studies showed that reactions of 2 and 3 with 9-ethylguanine gave rise selectively to SRu*RN* diastereomers. Dynamic chiral recognition of guanine can lead to high diastereoselectivity of DNA binding. The dinuclear complex 3 induced a large unwinding (31 degrees) of plasmid DNA, twice that of mononuclear 2 (14 degrees), and effectively inhibited DNA-directed RNA synthesis in vitro. This dinuclear complex gave rise to interstrand cross-links on a 213-bp plasmid fragment with efficiency similar to bifunctional cisplatin, and to 1,3-GG interstrand and 1,2-GG and 1,3-GTG intrastrand cross-links on site-specifically ruthenated 20-mers. Complex 3 blocked intercalation of ethidium considerably more than mononuclear 2. The concept of induced-fit recognition of DNA by organometallic complexes containing dynamic stereogenic centers via dynamic epimerization, intercalation, and cross-linking may be useful in the design of anticancer drugs.