Identification of (η6-arene)ruthenium(II) protein binding sites in E. coli cells by combined multidimensional liquid chromatography and ESI tandem mass spectrometry: specific binding of [(η6-p-cymene)RuCl2(DMSO)] to stress-regulated proteins and to helicases

The Protein-Binding Behavior of Platinum Anticancer Drugs in Blood Revealed by Mass Spectrometry

Cisplatin and its analogues are widely used as chemotherapeutic agents in clinical practice. After being intravenously administrated, a substantial amount of platinum will bind with proteins in the blood. This binding is vital for the transport, distribution, and metabolism of drugs; however, toxicity can also occur from the irreversible binding between biologically active proteins and platinum drugs. Therefore, it is very important to study the protein-binding behavior of platinum drugs in blood. This review summarizes mass spectrometry-based strategies to identify and quantitate the proteins binding with platinum anticancer drugs in blood, such as offline high-performance liquid chromatography/inductively coupled plasma mass spectrometry (HPLC–ICP-MS) combined with electrospray ionization mass spectrometry (ESI-MS/MS) and multidimensional LC–ESI-MS/MS. The identification of in vivo targets in blood cannot be accomplished without first studying the protein-binding behavior of platinum drugs in vitro; therefore, relevant studies are also summarized. This knowledge will further our understanding of the pharmacokinetics and toxicity of platinum anticancer drugs, and it will be beneficial for the rational design of metal-based anticancer drugs.

The interaction of half-sandwich (η5-Cp*)Rh(III) cation with histidine containing peptides and their ternary species with (N,N) bidentate ligands

Our goal was to explore the possible interactions of the potential metallodrug (η⁵-Cp*)Rh(III) complexes with histidine containing biomolecules (peptides/proteins) in order to understand the most important thermodynamic factors influencing the biospeciation and biotransformation of (η⁵-Cp*)Rh(III) complexes. To this end, here we report systematic solution thermodynamic and solution structural study on the interaction of (η⁵-Cp*)Rh(III) cation with histidine containing peptides and their constituents ((N-methyl)imidazole, GGA-OH, GGH-OH, histidine-amide, HGG-OH, GHG-NH₂), based on extensive ¹H NMR, ESI-MS and potentiometric investigations. The comparative evaluation of our data indicated that (η⁵-Cp*)Rh(III) cation is able to induce the deprotonation of amide nitrogen well below pH 7. Consequently, at physiological pH the peptides are coordinated to Rh(III) by tridentate manner, with the participation of amide nitrogen. At pH 7.4 the (η⁵-Cp*)Rh(III) binding affinity of peptides follow the order GGA-OH < < GGH-OH < < histidine-amide < HGG-OH < GHG-NH₂, i.e. the observed binding strength essentially depends on the presence and position of histidine within the peptide sequence. We also performed computational study on the possible solution structures of complexes present at near physiological pH. At pH 7.4 all histidine containing peptides form ternary complexes with strongly coordinating (N,N) bidentate ligands (ethylenediamine or bipyridyl), in which the peptides are monodentately coordinated to Rh(III) through their imidazole N¹‑nitrogens. In addition, the strongest chelators histidine-amide, HGG-OH and GHG-NH₂ are also able to displace these powerful bidentate ligands from the coordination sphere of Rh(III).

Metalloproteomics for molecular target identification of protein-binding anticancer metallodrugs

Proteomics has played an important role in elucidating the fundamental processes occuring in living cells. Translating these methods to metallodrug research ('metalloproteomics') has provided a means for molecular target identification of metal-based anticancer agents which should signifcantly advance the research field. In combination with biological assays, these techniques have enabled the mechanisms of action of metallodrugs to be linked to their interactions with molecular targets and aid understanding of their biological properties. Such investigations have profoundly increased our knowledge of the complex and dynamic nature of metallodrug-biomolecule interactions and have provided, at least for some compound types, a more detailed picture on their specific protein-binding patterns. This perspective highlights the progression of metallodrug proteomics research for the identification of non-DNA targets from standard analytical techniques to powerful metallodrug pull-down methods.

Enabling Methods to Elucidate the Effects of Metal-based Anticancer Agents

Next-generation metal-based pharmaceuticals are considered promising therapeutic agents, which may follow novel modes of action and engage with different targets compared to classical platinum(ii) anticancer agents. However, appropriate methods and assays are required to provide evidence of such unprecedented drug effects. Mass spectrometry (MS) has proved useful in probing the reactivity and selectivity of metal-based anticancer agents on a molecular level and recently also in the cellular context, especially with regard to the proteome. This chapter will discuss the design and use of competitive experiments to investigate activation pathways and binding preferences of metal-based anticancer agents by identifying reaction products via different MS setups. Moreover, cell-based approaches are described to obtain insights into novel potential targets and modes of action. Thus, mass spectrometry emerges as an enabling technology that connects molecules to mechanisms, highlighting the broad applicability of this analytical technique to the discovery and understanding of metal-based anticancer agents.

Selective binding of an organoruthenium complex to G-rich human telomeric sequence by tandem mass spectrometry

RATIONALE

Human telomeric DNA is reported to be a potential target for anticancer organometallic ruthenium(II) complexes, however, the interaction sites were not clearly discriminated and identified.

METHODS

In the current study, tandem mass spectrometry (MS/MS) using collision-induced dissociation (CID) was firstly introduced to identify the interaction sites of an organometallic ruthenium(II) complex [(η⁶ -biphenyl)Ru(en)Cl][PF₆ ] (1; en = ethylenediamine) with 5'-T₁ T₂ A₃ G₄ G₅ G₆ -3' (I), the repeating unit of human telomeric DNA, in both positive- and negative-ion mode at a low reaction molar ratio (1/I = 0.2) which was applied to preserve the site selectivity.

RESULTS

Mass spectrometric results showed that mono-ruthenated I was the main product under the conditions. In positive-ion mode, MS/MS results indicated that ruthenium complex 1 binds to T₂ or G₆ in strand I. However, in negative-ion mode, no efficient information was obtained for exact identification of ruthenation sites which may be attributed to losses of fragment ions due to charge neutralization by the coordination of the positively charged ruthenium complex to the short MS/MS fragments.

CONCLUSIONS

This is the first report of using top-down MS to characterize the interactions of organometallic ruthenium(II) complexes and human telomeric DNA. Thymine can be thermodynamically competitive with guanine for binding to ruthenium complexes even at low reaction molar ratio, which inspired us to explore in greater depth the significance of thymine binding.

Positive and negative nano-electrospray mass spectrometry of ruthenated serum albumin supported by docking studies: an integrated approach towards defining metallodrug binding sites on proteins

Negative mode nanoLC/nano ESI MS was used for determing Ru(ii) binding sites on protein.

Structure and reactivities of rhenium and technetium bis-arene sandwich complexes [M(η6-arene)2]+

Rhenium and ⁹⁹Tc bis-arene complexes for a molecule-based theranostic approach are presented. Conjugation of biovectors to benzene or substitution of naphthalene allows integration of {Re(η⁶-C₆H₆)}⁺ in pharmaceutical lead structures.

Quantification of bindings of organometallic ruthenium complexes to GSTπ by mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) has been widely used to identify binding sites of metal complexes to proteins. However, the MS quantification of the metal-protein coordination remains a challenge. We have recently demonstrated by ESI-MS analysis that organometallic ruthenium complexes [(η(6)-arene)Ru(en)Cl](+) (arene=p-cymene (1), biphenyl (2) or 9,10-dihydrophenanthrene (3); en=ethylenediamine) bound to human glutathione-S-transferase π (GSTπ) at Cys15 and Cys48 within the G-site, and Cys102 and Met92 on the interface of the GSTπ dimer, showing inhibitory potency against the enzyme (J. Inorg. Biochem., 128 (2013) 77-84). Herein, we developed a mass spectrometric method to quantify the binding stoichiometry of the three complexes to GSTπ. The differences in signal intensities of the heavy-labelled peptides produced by tryptic digestion of the ruthenated GSTπ complexes and the respective light-labelled peptides in the tryptic digest of equimolar GSTπ were used to calculate the binding stoichiometry at specific residues. The results indicated that the pre-complexation of GSTπ with its substrate GSH significantly reduced the bindings of the ruthenium complexes at Met92 and Cys102, but had little impact on the bindings at Cys15 and Cys48. As the inhibitory activities of the ruthenium complexes against GSTπ are similar to those against GSTπ in complexation with GSH, these results suggest that the inhibition of the ruthenium complexes on GSTπ is attributed to the ruthenation at Cys15 and Cys48. The present work provides not only insights into the understanding on the inhibitory mechanism of ruthenium complexes GSTπ, but also a general method for quantitative characterization of metal-protein interactions.

Metallomic and metalloproteomic strategies in elucidating the molecular mechanisms of metallodrugs

Metals play a critical role in life processes, and metal-based drugs nowadays have been commonly used for therapeutic and diagnostic purposes. However, severe side-effects and acquired drug resistance are the major issues needing to be resolved prior to more effective metallodrugs being developed, which requires a full understanding of the underlying molecular mechanisms. Metallomic and metalloproteomic approaches have received growing attention and have been implemented in inorganic medicinal chemistry and chemical biology in the endeavor to expand our knowledge of the pharmacological profiles, potential targets and functional pathways of metallodrugs. This perspective summarizes some recent progress in using metallomic and metalloproteomic strategies to elucidate the mechanisms of action of representative anticancer and antimicrobial metal-based drugs and agents.

Application of mass spectrometric techniques to delineate the modes-of-action of anticancer metallodrugs

Mass spectrometry (MS) has emerged as an important tool for studying anticancer metallodrugs in complex biological samples and for characterising their interactions with biomolecules and potential targets on a molecular level. The exact modes-of-action of these coordination compounds and especially of next generation drug candidates have not been fully elucidated. Due to the fact that DNA is considered a crucial target for platinum chemotherapeutics, metallodrug-DNA binding studies dominated the field for a long time. However, more recently, alternative targets were considered, including enzymes and proteins that may play a role in the overall pharmacological and toxicological profile of metallodrugs. This review focuses on MS-based techniques for studying anticancer metallodrugs in vivo, in vitro and in situ to delineate their modes-of-action.

Folates are potential ligands for ruthenium compounds in vivo

A labile ruthenium(ii) complex has been observed to chelate to folates under physiologically relevant conditions. The diastereomeric complexes formed would interfere with the one-carbon carrying role of folate in vivo. This highlights the importance of considering small molecules alongside macromolecules when determining the chemical origins of cytotoxicity of metallodrug candidates.

Competitive binding sites of a ruthenium arene anticancer complex on oligonucleotides studied by mass spectrometry: ladder-sequencing versus top-down

We report identification of the binding sites for an organometallic ruthenium anticancer complex [(η (6)-biphenyl)Ru(en)Cl][PF6] (1; en = ethylenediamine) on the 15-mer single-stranded oligodeoxynucleotides (ODNs), 5'-CTCTCTX7G8Y9CTTCTC-3' [X = Y = T (I); X = C and Y = A (II); X = A and Y = T (III); X = T and Y = A (IV)] by electrospray ionization mass spectrometry (ESI-MS) in conjunction with enzymatic digestion or tandem mass spectrometry (top-down MS). ESI-MS combined with enzymatic digestion (termed MS-based ladder-sequencing), is effective for identification of the thermodynamically-favored G-binding sites, but not applicable to determine the thermodynamically unstable T-binding sites because the T-bound adducts dissociate during enzymatic digestion. In contrast, top-down MS is efficient for localization of the T binding sites, but not suitable for mapping ruthenated G bases, due to the facile fragmentation of G bases from ODN backbones prior to the dissociation of the phosphodiester bonds. The combination of the two MS approaches reveals that G8 in each ODN is the preferred binding site for 1, and that the T binding sites of 1 are either T7 or T11 on I and IV, and either T6 or T11 on II and III, respectively. These findings not only demonstrate for the first time that T-bases in single-stranded oligonucleotides are kinetically competitive with guanine for such organoruthenium complexes, but also illustrate the relative merits of the combination of ladder-sequencing and top-down MS approaches to elucidate the interactions of metal anticancer complexes with DNA.

Evaluation of arene ruthenium(II) N-heterocyclic carbene complexes as organometallics interacting with thiol and selenol containing biomolecules

Metal complexes with N-heterocyclic carbene (NHC) ligands have been widely used in catalytic chemistry and are now increasingly considered for the development of new chemical tools and metal based drugs. Ruthenium complexes of the type (p-cymene)(NHC)RuCl(2) interacted with biologically relevant thiols and selenols, which resulted in the inhibition of enzymes such as thioredoxin reductase or cathepsin B. Pronounced antiproliferative effects could be obtained provided that an appropriate cellular uptake was achieved. Inhibition of tumor cell growth was accompanied by a perturbation of metabolic parameters such as cellular respiration.

Sensitive Marker of the Cisplatin-DNA Interaction: X-Ray Photoelectron Spectroscopy of CL

The development of cisplatin and Pt-based analogues anticancer agents requires knowledge concerning the molecular mechanisms of interaction between such drugs with DNA. However, the binding dynamics and kinetics of cisplatin reactions with DNA determined by traditional approaches are far from satisfactory. In this study, a typical 20-base oligonucleotide (CGTGACAGTTATTGCAGGCG), as a simplified model representing DNA, was mixed with cisplatin in different molar ratios and incubation time. High-resolution XPS spectra of the core elements C, N, O, P, and Cl were recorded to explore the interaction between cisplatin and DNA. From deconvoluted Cl spectra we could readily differentiate the covalently bound chlorine from ionic chloride species in the cisplatin-oligo complexes, which displayed distinct features at various reaction times and ratios. Monitoring the magnitude and energy of the photoelectron Cl 2p signal by XPS could act as a sensitive marker to probe the interaction dynamics of chemical bonds in the reaction of cisplatin with DNA. At 37°C, the optimum incubation time to obtain a stable cisplatin-oligo complex lies around 20 hrs. This novel analysis technique could have valuable implications to understand the fundamental mechanism of cisplatin cytotoxicity and determine the efficiency of the bonds in treated cancer cells.

Anticancer metallodrug research analytically painting the "omics" picture--current developments and future trends

Anticancer metallodrug development has for a long time been characterised by the similarity of new drug candidates to cisplatin and DNA as the primary target. Recent advances in bioanalytical techniques with high sensitivity and selectivity have revealed that metal-based drugs can undergo a wide range of biomolecular interactions beyond DNA and have generated interest in proteins as possible targets for metallodrugs. In fact, implementation of metallomics approaches that are able to reveal the fate of the compounds in biological systems can help to move drug development towards more targeted and rational design of novel metallodrugs. Additionally, proteomic screening and gene expression analysis can provide insight into physiological response to drug treatment and identify the reasons for drug resistance. Herein, we review selected applications which led to a better understanding of the mode of action of clinically established metal-based anticancer agents and novel metallodrug candidates.

Differences in the cellular response and signaling pathways between cisplatin and monodentate organometallic Ru(II) antitumor complexes containing a terphenyl ligand

The new monofunctional Ru(II)-arene complex [(η⁶-arene)Ru(II)(en)Cl]+, where en = 1,2-diaminoethane and the arene is para-terphenyl (complex 1) exhibits promising cytotoxic effects in human tumor cells including those resistant to conventional cisplatin (J. Med. Chem.2008, 51, 5310). The present study is focused on the cellular pharmacology of 1 to elucidate more deeply the mechanisms underlying its antitumor effects. We have identified several cellular mechanisms induced by 1 in human ovarian carcinoma cells, including inhibition of DNA synthesis, overexpression and activation of p53, expression of proapoptotic proteins p21(WAF1) and Bax, G₀/G₁ arrest, and nuclear fragmentation as a result of apoptotic, and, to a much lower extent, also necrotic processes. Thus, 1 inhibits growth of the cancer cells through induction of apoptotic cell death and G₀/G₁ cell cycle arrest. Further investigations have shown that 1 induces apoptosis by regulating the expression of Bcl-2 family proteins. There were significant differences in cellular responses to the treatment with 1 and with conventional cisplatin, particularly in the kinetics and the extent of these responses. In addition, the distinct p53 activation profile of 1 compared with cisplatin provides an explanation for the activity of this ruthenium drug against cisplatin-resistant cells. Hence complex 1 may provide an alternative therapy in patients with acquired cisplatin resistance, particularly with respect to its very low mutagenicity and different mode of action compared to platinum antitumor drugs in clinical use.

Inductive properties of polypyridyl ruthenium complexes significantly regulate various protein distributions in Escherichia coli

Ruthenium complexes with similar octahedral structures but different intrinsic inductive properties significantly influence the total cellular protein distributions, which may affect different metabolic pathways. A systematic study of the relationship between ruthenium complexes and Escherichia coli was undertaken, using two-dimensional gel electrophoresis analysis and the identification of various proteins by mass data mining. Based on the low similarities (<40%) between the total protein distributions, the inductive properties of the ruthenium complexes are relevant to the formation of the protein-Ru interaction in addition to the Ru-DNA interaction. Two major protein functions in E. coli BL21 that were reduced by compound 1 were oxidoreductases and transporters, corresponding to 29% and 25% of the 24 down-regulated proteins. The main biological processes of the proteins down-regulated by compound 1 were related to carbohydrate reactions, including in transport, tricarboxylic acid (TCA) cycle, glycolysis, and gluconeogenesis. All four ruthenium complexes shared similar up-regulated proteins, including clpB and kpyk1, and down-regulated similar proteins, including ompA and ybbN. This result supports that the presence of Ru-protein interactions is a major factor affecting bacteria growth, and particularly transport and carbohydrate-related reactions.

Reactivity of anticancer metallodrugs with serum proteins: new insights from size exclusion chromatography-ICP-MS and ESI-MS

A method based on the coupling of high resolution size-exclusion liquid chromatography using a polymer stationary phase with inductively coupled plasma mass spectrometry was developed to study the interactions of two metallodrugs - cisplatin and RAPTA-T - with the serum proteins albumin and transferrin. In contrast to previous approaches, the technique allowed the total recovery of the metals from the column and was able to discriminate between the different species of the metallodrugs and their complexes with the proteins at femtomolar detection levels. Metal binding was found to be dependent on the protein concentration and on the incubation time of the sample. Cisplatin was found to bind the serum proteins to the same extent, whereas RAPTA-T showed marked preference for transferrin. The affinity of the ruthenium complex for holo-transferrin was higher than for the apo-form suggesting a cooperative iron-mediated metal binding mechanism. RAPTA-T binding to holo-transferrin was further investigated by electrospray mass spectrometry using both the intact protein and a model peptide mimicking the iron-binding pocket.

Reaction of the Anticancer Organometallic Ruthenium Compound, [(eta-p-Cymene)Ru(ATSC)Cl]PF(6) with Human Serum Albumin

The reaction of [(eta(6)-p-cymene)Ru(ATSC)Cl]PF(6) (ATSC = 9-anthraldehyde thiosemicarbazone) with human serum albumin was investigated at different temperatures using fluorescence and infrared spectrophotometry. The binding constant, K, for the reaction was determined using a number of different methods. Using a modified Stern-Volmer equation, K was determined to be 9.09 x 10(4), 12.1 x 10(4), and 13.1 x 10(4) M(-1) at 293 K, 298 K, and 308 K, respectively. A thermodynamic analysis showed that the reaction is spontaneous with DeltaG being negative. The enthalpy of reaction DeltaH = 16.5kJ mol(-1) and the entropy of reaction DeltaS = 152 Jmol(-1)K(-1). The values of DeltaH and DeltaS suggest that hydrophobic forces are dominant in the mode of interaction and that the process is mostly entropy driven.

Tuning heavy metal compounds for anti-tumor activity: is diversity the key to ruthenium’s success?

This review aims to bring the reader up to date with the more recent ruthenium compounds that have been synthesized and tested for their cytotoxicity. The chemistry of these transition metal complexes will be introduced and the basic principles that govern their common behavior outlined. The recent history of established compounds within this field will be presented alongside those that now represent the cutting-edge. The inherent variety within this class of compounds will lead the reader to appreciate their diversity and pose questions as to their similarities aside from the presence of a shared metal ion. This review aims to discuss and contextualize the state-of-the-art research within the context of the speculative advancement of this developing field. There is an evident need to specify the molecular and cellular targets of these drug molecules in order to ultimately elucidate their mode or modes of action. The evidence presented herein suggests that new avenues of research require novel analytical probes and methods for tracing the fate of ruthenium complexes in cells in order to understand their very promising cytotoxic activity.

Exploring metallodrug-protein interactions by mass spectrometry: comparisons between platinum coordination complexes and an organometallic ruthenium compound

Electrospray ionisation mass spectrometry was used to analyse the reactions of metal compounds with mixtures of selected proteins. Three representative medicinally relevant compounds, cisplatin, transplatin and the organometallic ruthenium compound RAPTA-C, were reacted with a pool of three proteins, ubiquitin, cytochrome c and superoxide dismutase, and the reaction products were analysed using high-resolution mass spectrometry. Highly informative electrospray ionisation mass spectra were acquired following careful optimisation of the experimental conditions. The formation of metal-protein adducts was clearly observed for the three proteins. In addition, valuable information was obtained on the nature of the protein-bound metallofragments, on their distribution among the three different proteins and on the binding kinetics. The platinum compounds were less reactive and considerably less selective in protein binding than RAPTA-C, which showed a high affinity towards ubiquitin and cytochrome c, but not superoxide dismutase. In addition, competition studies between cisplatin and RAPTA-C showed that the two metallodrugs have affinities for the same amino acid residues on protein binding.