Consequences of nucleic acid conformation on the binding of a trinuclear platinum drug

Dinuclear Organoruthenium Complex for Mitochondria-Targeted Near-Infrared Imaging and Anticancer Therapy to Overcome Platinum Resistance

New mononuclear and dinuclear Ru(II) coordination compounds with the 2,7-bisbenzoimidazolyl-naphthyridine ligand have been synthesized and characterized by UV-vis, NMR, and MALDI-TOF. The molecular structures for Ru(II) compounds were determined by single-crystal X-ray diffraction. With the expansion of ligand π-conjugation and the increase in the complexed Ru number, the maximum emission wavelength red-shifted from 696 to 786 nm. The binding mode between complexes and DNA was predicted by molecular docking, which is intercalations and π-π stacking interactions with the surrounding bases. The intercalation mode of DNA binding was then determined by DNA titration and ethidium bromide (EB) displacement experiments. The antigrowth effects of complexes RuY, RuY1, and RuY2 were tested in HaCat (normal cells), HeLa (cervical cancer), A549 (lung cancer), and A549/DDP (cisplatin-resistant lung cancer) through the MTT assay. The dinuclear complex RuY2 was superior to mononuclear complexes and cisplatin in the cisplatin-resistant cell line. Confocal imaging proved that the subcellular localization of Ru(II) complexes was mitochondria; moreover, apoptosis was detected by flow cytometry. All three complexes showed a dose-dependent manner in all four cell lines. All Ru(II) complexes were found to have reactive oxygen species (ROS). The finding indicated that these Ru(II) complexes caused cell death by both DNA disruption and ROS. This study helps to explore the potential of the polynuclear Ru(II) complexes for the combination of NIR imaging and Pt-resistant cancer therapy.

Nano-Based Systems and Biomacromolecules as Carriers for Metallodrugs in Anticancer Therapy

Since the discovery of cisplatin and its potency in anticancer therapy, the development of metallodrugs has been an active area of research. The large choice of transition metals, oxidation states, coordinating ligands, and different geometries, allows for the design of metal-based agents with unique mechanisms of action. Many metallodrugs, such as titanium, ruthenium, gallium, tin, gold, and copper-based complexes have been found to have anticancer activities. However, biological application of these agents necessitates aqueous solubility and low systemic toxicity. This minireview highlights the emerging strategies to facilitate the in vivo application of metallodrugs, aimed at enhancing their solubility and bioavailability, as well as improving their delivery to tumor tissues. The focus is on encapsulating the metal-based complexes into nanocarriers or coupling to biomacromolecules, generating efficacious anticancer therapies. The delivery systems for complexes of platinum, ruthenium, copper, and iron are discussed with most recent examples.

Computational investigations of trans‑platinum(II) oxime complexes used as anticancer drug

Some platinum oxime complexes are optimized at HF/CEP-31G level which has been reported as the best level for these type complexes in the gas phase. IR spectrum is calculated and the new scale factor is derived. NMR spectrum is calculated at the same level of theory and examined in detail. Quantum chemical parameters which have been mainly used are investigated and their formulas are given in detail. Additionally, selected quantum chemical parameters of studied complexes are calculated. New theoretical IC₅₀% formulas are derived and biological activity rankings of mentioned complexes are investigated.

Current State of Metal-Based Drugs for the Efficient Therapy of Lung Cancers and Lung Metastases

Lung cancer is the second most common cancer in both men and women and thus a leading cause of cancer-related deaths worldwide. New efficient treatments especially for its advanced stages and metastases are desperately needed, particularly with regard to overcoming the resistance which thwarts the efficacy of most clinically established drugs such as the platinum complexes. Glimpses of hope are new metal-based drugs that have emerged over the past decade which displayed efficacy in patients with platinum-resistant tumors and metastases. This chapter provides an overview of the latest developments of such metal-based drugs against lung cancer.

Metal complex interactions with DNA

Increasing numbers of DNA structures are being revealed using a diverse range of transition metal complexes and biophysical spectroscopic techniques. Here we present a review of metal complex-DNA interactions in which several binding modes and DNA structural forms are explored.

Platinum and Palladium Polyamine Complexes as Anticancer Agents: The Structural Factor

Since the introduction of cisplatin to oncology in 1978, Pt(II) and Pd(II) compounds have been intensively studied with a view to develop the improved anticancer agents. Polynuclear polyamine complexes, in particular, have attracted special attention, since they were found to yield DNA adducts not available to conventional drugs (through long-distance intra- and interstrand cross-links) and to often circumvent acquired cisplatin resistance. Moreover, the cytotoxic potency of these polyamine-bridged chelates is strictly regulated by their structural characteristics, which renders this series of compounds worth investigating and their synthesis being carefully tailored in order to develop third-generation drugs coupling an increased spectrum of activity to a lower toxicity. The present paper addresses the latest developments in the design of novel antitumor agents based on platinum and palladium, particularly polynuclear chelates with variable length aliphatic polyamines as bridging ligands, highlighting the close relationship between their structural preferences and cytotoxic ability. In particular, studies by vibrational spectroscopy techniques are emphasised, allowing to elucidate the structure-activity relationships (SARs) ruling anticancer activity.

Novel oximato-bridged platinum(II) di- and trimer(s): synthetic, structural, and in vitro anticancer activity studies

Novel platinum complexes of trans geometry [PtCl(2){(Z)-R(H)C═NOH}(2)] [R = Me (1), Et (3)] and [PtCl(2){(E)-R(H)C═NOH}{(Z)-R(H)C═NOH}] [R = Me (2), Et (4)] as well as the classic trans-[PtCl(2)(R(2)C═NOH)(2)] [R = Me, Et] were reacted with an equivalent amount of silver acetate in acetone solution at ambient temperature, resulting in formation of unprecedented head-to-tail-oriented oximato-bridged dimers [PtCl{μ-(Z)-R(H)C═NO}{(Z)-R(H)C═NOH}](2) [R = Me (5), Et (7)], [PtCl{μ-(Z)-R(H)C═NO}{(E)-R(H)C═NOH}](2) [R = Me (6), Et (8)], and [PtCl(μ-R(2)C═NO)(R(2)C═NOH)](2) [R = Me (9), Et (10)], correspondingly. The dimeric species feature a unique six-membered diplatinacycle and represent the first example of oxime ligands coordinated to platinum via the oxygen atom. All complexes were characterized by elemental analyses, electrospray ionization mass spectrometry, IR and multinuclear ((1)H, (13)C, and (195)Pt) NMR spectroscopy, as well as X-ray diffraction in the cases of dimers 6 and 9. Furthermore, the crystal and molecular structures of a trimeric oximato-bridged complex 11 comprising three platinum units connected in a chain way were established. The cytotoxicity of both dimers and the respective monomers was comparatively evaluated in three human cancer cell lines: cisplatin-sensitive CH1 cells as well as cisplatin-resistant SW480 and A549 cells, whereupon structure-activity relationships were drawn. Thus, it was found that dimerization results in a substantial (up to 7-fold) improvement of IC(50) values of (aldoxime)Pt(II) compounds, whereas for the analogous complexes featuring ketoxime ligands the reverse trend was observed. Remarkably, the novel dimers yielded no cross-resistance with cisplatin in SW480 cells, exhibiting up to 2-fold enhanced cytotoxicity in comparison with the CH1 cell line and thereby possessing a promising potential to overcome resistance toward platinum anticancer drugs. The latter point was also confirmed by investigating the potency of apoptosis induction in the case of one monomer as well as one dimer; the investigated complexes proved to be strong apoptotic agents which could induce cell death even in the cisplatin-resistant SW480 cell line.

Reactivity of a cytostatic active N,N-donor-containing dinuclear Pt(II) complex with biological relevant nucleophiles

A dinuclear platinum(II) complex that was recently investigated in our group was tested for its cytostatic activity and found to be active against HeLa S3 cells. The complex consists of a bidentate N,N-donor chelating ligand system in which the two platinum centers are connected by an aliphatic chain of 10 methylene groups. The complex [Pt(2)(N(1),N(10)-bis(2-pyridylmethyl)-1,10-decanediamine)(OH(2))(4)](4+) (10NNpy) is of further special interest, since only little is known about the substitution behavior of such dinuclear platinum complexes that contain a bidentate coordination sphere. The complex was investigated using different biologically relevant nucleophiles, such as thiourea (tu), L-methionine (L-Met), glutathione (GSH), and guanine-5'-monophosphate (5'-GMP), at two different pH values (2 and 7.4). The substitution of coordinated water by these nucleophiles was studied under pseudo-first-order conditions as a function of nucleophile concentration, temperature, and pressure, using stopped-flow techniques and UV-vis spectroscopy. The reactivity of 10NNpy with the selected nucleophiles was found to be tu ≫ 5'-GMP > L-Met > GSH at pH 2 and GSH > tu > L-Met at pH 7.4. The results for the dinuclear 10NNpy complex were compared to those for the corresponding mononuclear reference complex [Pt(aminomethylpyridine)(OH(2))(2)](2+), Pt(amp), studied before in our group, by which the effect of the addition of an aliphatic chain, an increase in the overall charge, and a shift in the pK(a) values of the coordinated water ligands could be investigated. The reactivity order for Pt(amp) was found to be tu > GSH > L-Met at pH 7.4.

Excursions in polynuclear platinum DNA binding

Polynuclear platinum agents are a structurally unique class of anti-cancer drugs, distinct from the cisplatin family. To describe the chemistry and biology of this class, it was necessary to challenge the accepted paradigms for the structure-activity relationships; design new chemotypes and delineate the structures and consequences of their DNA binding modes. This article summarizes the structural changes induced in DNA by both covalent (bond-forming) and non-covalent (ligand recognition) adducts. Solution (Nuclear Magnetic Resonance), solid state (crystallography) and gas-phase (Electrospray Ionization Mass Spectrometry) techniques have all been used to describe the new DNA structures along with molecular biological techniques. The combined approaches allow molecular description of hitherto unobserved adducts such as long-range major-groove interstrand crosslinks; directional isomers on DNA and a third class of ligand-DNA binding, the phosphate clamp. The phosphate recognition is distinct from ''classic'' minor-groove recognition or intercalation.

Drug delivery of lipophilic pyrenyl derivatives by encapsulation in a water soluble metalla-cage

The self-assembly of 2,4,6-tris(pyridin-4-yl)-1,3,5-triazine (tpt) triangular panels with p-cymene (p-Pr(i)C(6)H(4)Me) ruthenium building blocks and 2,5-dioxydo-1,4-benzoquinonato (dobq) bridges, in the presence of a functionalised pyrenyl derivative (pyrene-R), affords the triangular prismatic host-guest compounds [(pyrene-R) [symbol: see text] Ru(6)(p-Pr(i)C(6)H(4)Me)(6)(tpt)(2)(dobq)(3)](6+) ([(pyrene-R) [symbol: see text] 1](6+)). The inclusion of eight mono-substituted pyrenyl derivatives including biologically relevant structures (a = 1-pyrenebutyric acid, b = 1-pyrenebutanol, c = 1-pyrenemethylamine, d = 1-pyrenemethylbutanoate, e = 1-(4,6-dichloro-1,3,5-triazin-2-yl)pyrene, f = N-hexadecylpyrene-1-sulfonamide, g = pyrenyl ethacrynic amide and h = 2-(pyren-1-ylmethylcarbamoyl) phenyl acetate), and a di-substituted pyrenyl derivative (i = 1,8-bis(3-methyl-butyn-1-yl-3-ol)pyrene), has been accomplished. The carceplex nature of these systems with the pyrenyl moiety being firmly encapsulated in the hydrophobic cavity of the cage with the functional groups pointing outwards was confirmed by NMR ((1)H, 2D, DOSY) spectroscopy and electrospray ionization mass spectrometry (ESI-MS). The cytotoxicities of these water-soluble compounds have been established using human ovarian A2780 cancer cells. All the host-guest systems are more cytotoxic than the empty cage itself [1][CF(3)SO(3)](6) (IC(50) = 23 microM), the most active carceplex [f [symbol: see text] 1][CF(3)SO(3)](6) is an order of magnitude more cytotoxic.

The status of platinum anticancer drugs in the clinic and in clinical trials

Since its approval in 1979 cisplatin has become an important component in chemotherapy regimes for the treatment of ovarian, testicular, lung and bladder cancers, as well as lymphomas, myelomas and melanoma. Unfortunately its continued use is greatly limited by severe dose limiting side effects and intrinsic or acquired drug resistance. Over the last 30 years, 23 other platinum-based drugs have entered clinical trials with only two (carboplatin and oxaliplatin) of these gaining international marketing approval, and another three (nedaplatin, lobaplatin and heptaplatin) gaining approval in individual nations. During this time there have been more failures than successes with the development of 14 drugs being halted during clinical trials. Currently there are four drugs in the various phases of clinical trial (satraplatin, picoplatin, Lipoplatin and ProLindac). No new small molecule platinum drug has entered clinical trials since 1999 which is representative of a shift in focus away from drug design and towards drug delivery in the last decade. In this perspective article we update the status of platinum anticancer drugs currently approved for use, those undergoing clinical trials and those discontinued during clinical trials, and discuss the results in the context of where we believe the field will develop over the next decade.

The role of bridging ligands in determining DNA-binding ability and cross-linking patterns of dinuclear platinum(II) antitumour complexes

The DNA binding ability and binding mode of platinum complexes are crucial factors that govern their cytotoxic activity. In this work, circular dichroism spectroscopy, gel electrophoresis and MALDI-TOF MS spectrometry combined with enzymatic degradation have been used to elucidate the role of bridging ligands in DNA-binding ability and cross-linking patterns of two dinuclear antitumour active platinum(II) complexes, {[cis-Pt(NH(3))(2)Cl](2)L1}(NO(3))(2) (1, L1= 4,4'-methylenedianiline) and {[cis-Pt(NH(3))(2)Cl](2)L2}(NO(3))(2) (2, L2 = alpha,alpha'-diamino-p-xylene). Although both complexes have two cis-diammine-Pt(II) moieties (1,1/c,c), complex 1 exhibits much higher DNA-binding ability than complex 2. The former readily forms both 1,3- and 1,4-intrastrand cross-links with DNA oligonucleotides, while the latter preferentially forms 1,4- rather than 1,3-intrastrand cross-links. Cytotoxicity studies against a human non-small-cell lung cancer cell line (A549) demonstrate that complex 1 has higher activity than 2. These results show that the linker properties play a critical role in controlling the DNA-binding and cross-linking abilities and in modulating the cytotoxicity of dinuclear platinum complexes.

Effects of geometric isomerism and anions on the kinetics and mechanism of the stepwise formation of long-range DNA interstrand cross-links by dinuclear platinum antitumor complexes

Reported herein is a detailed study of the kinetics and mechanism of formation of a 1,4-GG interstrand cross-link by the dinuclear platinum anticancer compound [15N][{cis-PtCl(NH3)2}2{mu-NH2(CH2)6NH2}]2+ (1,1/c,c (1)). The reaction of [15N]1 with 5'-{d(ATATGTACATAT)2} (I) has been studied by [1H,15N] HSQC NMR spectroscopy in the presence of different concentrations of phosphate. In contrast with the geometric trans isomer (1,1/t,t), there was no evidence for an electrostatic preassociation of 1,1/c,c with the polyanionic DNA surface, and the pseudo-first-order rate constant for the aquation of [(15)N]1 was actually slightly higher (rather than lower) than that in the absence of DNA. When phosphate is absent, the overall rate of formation of the cross-link is quite similar for the two geometric isomers, occurring slightly faster for 1,1/t,t. A major difference in the DNA binding pathways is the observation of phosphate-bound intermediates only in the case of 1,1/c,c. 15 mM phosphate causes a dramatic slowing in the overall rate of formation of DNA interstrand cross-links due to both the slow formation and slow closure of the phosphate-bound monofunctional adduct. A comparison of the molecular models of the bifunctional adducts of the two isomers shows that helical distortion is minimal and globally the structures of the 1,4 interstrand cross-links are quite similar. The effect of carrier ligand was investigated by similar studies of the ethylenediamine derivative [15N]1-en. A pKa value of 5.43 was determined for the [15N]1,1/c,c-en diaquated species. The rate of reaction of [15N]1-en with duplex I is similar to that of 1,1/c,c and the overall conformation of the final adduct appears to be similar. The significance of these results to the development of "second-generation" polynuclear platinum clinical candidates based on the 1,1/c,c chelate (dach) series is discussed.

Improving platinum(II)-based anticancer drug delivery using cucurbit[n]urils

Despite the synthesis of hundreds of new platinum(II) and platinum(IV)-based complexes each year as potential anticancer drugs, only three have received world-wide approval: cisplatin, carboplatin and oxaliplatin. The next big advance in platinum-based chemotherapy is not likely to come from the development of new drugs, but from the controlled and targeted delivery of already approved drugs or those in late stage clinical trials. Encapsulation of platinum drugs inside macromolecules has already demonstrated promise, and encapsulation within cucurbit[n]urils has shown particular potential. Partial or full encapsulation within cucurbit[n]urils provides steric hindrance to drug degradation by peptides and proteins, and the use of different sized cucurbit[n]urils allows for the tuning of drug release rates, cytotoxicity and toxicity.

A dinuclear monofunctional platinum(II) complex with an aromatic linker shows low reactivity towards glutathione but high DNA binding ability and antitumor activity

Multinuclear Pt(II) complexes represent a novel class of antitumor agents. In this work, a dinuclear monofunctional Pt(II) complex {[cis-Pt(NH(3))(2)Cl](2)(4,4'-methylenedianiline)}(NO(3))(2) (1) was synthesized and characterized by (1)H NMR, electrospray mass spectrometry, and elemental analysis. The 2D [(1)H,(15)N] heteronuclear single quantum coherence NMR spectra of (15)N-labeled 1 revealed that the cationic core of this water-soluble complex hardly hydrolyzes in aqueous solution and reacts very slowly with glutathione. Hydrolysis appears not to be an essential step for the formation of Pt-guanosine-5'-monophosphate (5'-GMP) or Pt-DNA adducts because the complex can react readily with 5'-GMP and partially transform B-DNA into its Z form. Such properties are desired to achieve the goal of enhancing cytotoxicity and lowering side effects of Pt(II) complexes. In fact, complex 1 is highly cytotoxic against the murine leukemia (P-388) and the human non-small-cell lung cancer (A-549) cell lines, and it is more cytotoxic than cisplatin at most concentrations tested.

Metal-based anticancer drugs: From a past anchored in platinum chemistry to a post-genomic future of diverse chemistry and biology

The field of metal-based anticancer drugs was initiated by cisplatin, one of the leading agents in clinical use. Cisplatin acts by binding to DNA and forming 1,2 intrastrand cross-links. Its importance is reflected by the fact that it is estimated that 50-70 % of cancer patients are treated with a platinum drug [7]. For some time, molecular designs in the metallo-drug field remained obdurately anchored in cis-diamine platinum(II) chemistry, but now the field is evolving rapidly with a variety of alternate and very diverse designs being explored. These designs give rise to new spectra of activity and potency and can circumvent cisplatin resistance. This critical review considers the existing clinical platinum drugs, and those currently in commercial development, alongside the new designs including ruthenium anticancer and antimetastatic drugs in clinical trials, polynuclear drugs, organometallic drugs, titanium and gallium drugs, and emerging supramolecular metallo-drugs that act on DNA by noncovalent interactions. The rapid evolution of the field is being informed by post-genomic knowledge and approaches, and further dramatic step-change breakthroughs can be expected as a result; harnessing this knowledge and responding to and taking advantage of this new environment requires integration of chemistry and biology research.

Mass Measurement Accuracy in Analyses of Highly Complex Mixtures Based Upon Multidimensional Recalibration

Mass spectrometry combined with a range of on-line separation techniques has become a powerful tool for characterization of complex mixtures, including protein digests in proteomics studies. Accurate mass measurements can be compromised due to variations that occur in the course of an on-line separation, e.g., due to excessive space charge in an ion trap, temperature changes, or other sources of instrument "drift". We have developed a multidimensional recalibration approach that utilizes existing information on the likely mixture composition, taking into account variable conditions of mass measurements, and that corrects the mass calibration for sets of individual peaks binned by, for example, the total ion count for the mass spectrum, the individual peak abundance, m/z value, and liquid chromatography separation time. The multidimensional recalibration approach uses a statistical matching of measured masses in such measurements, often exceeding 105, to a significant number of putative known species likely to be present in the mixture (i.e., having known accurate masses), to identify a subset of the detected species that serve as effective calibrants. The recalibration procedure involves optimization of the mass accuracy distribution (histogram), to provide a more confident distinction between true and false identifications. We report the mass accuracy improvement obtained for data acquired using a TOF and several FTICR mass spectrometers. We show that the multidimensional recalibration better compensates for systematic mass measurement errors and also significantly reduces the mass error spread: i.e., both the accuracy and precision of mass measurements are improved. The mass measurement improvement is found to be virtually independent of the initial instrument calibration, allowing, for example, less frequent calibration. We show that this recalibration can provide sub-ppm mass measurement accuracy for measurements of a complex fungal proteome tryptic digest and provide improved confidence or numbers of peptide identifications.

Effects of geometric isomerism in dinuclear platinum antitumor complexes on aquation reactions in the presence of perchlorate, acetate and phosphate

The aquation and subsequent reactions of the dinuclear Pt antitumor complexes [{trans-PtCl(NH(3))(2)}(2)(mu-NH(2)(CH(2))(6)NH(2))](2+) (1,1/t,t) and [{cis-PtCl(NH(3))(2)}(2)(mu-NH(2)(CH(2))(6)NH(2))](2+) (1,1/c,c) in 15 mM perchlorate, acetate or phosphate solutions were followed at 298 K by [(1)H,(15)N] HSQC 2D NMR spectroscopy. Rate and equilibrium constants for the initial reversible aquation and the subsequent reversible reaction with phosphate or acetate are reported. The rate constant for the first aquation step is two-fold lower for 1,1/c,c than 1,1/t,t but the anation rate constants are similar so that the equilibrium lies further towards the chloro form for the 1,1/c,c compound. A pK (a) value of 6.01+/-0.03 was determined for the diaquated species [{cis-Pt(NH(3))(2)(H(2)O)}(2)(mu-NH(2)(CH(2))(6)NH(2))](4+) (1,1/c,c-3) which is 0.4 units higher than that of the 1,1/t,t compound. The rate constants for the binding of acetate and phosphate to 1,1/t,t are similar, but the rate constant for the reverse reaction is close to ten-fold higher in the case of phosphate so that equilibrium conditions are attained more rapidly (12 h compared with 64 h). On the other hand, for 1,1/c,c the rate constants for the forward and reverse reactions with acetate and phosphate are quite similar so that equilibrium conditions are reached very slowly (80-100 h) and a greater proportion of phosphate-bound species are present. The reduced lability of the bound phosphate for 1,1/c,c is attributed to the formation of a macrochelate phosphate-bridged species which was characterized by (31)P NMR and ESI-MS. The speciation profiles of 1,1/t,t and 1,1/c,c under physiological conditions are explored.

Analysis of nucleic acids by FTICR MS

Fourier transform ion cyclotron resonance (FTICR) mass spectrometry represents a unique platform with which to study nucleic acids and non-covalent complexes containing nucleic acids moieties. In particular, systems in which very high mass measurement accuracy is required, very complex mixtures are to be analyzed, or very limited amounts of sample are available may be uniquely suited to interrogation by FTICR mass spectrometry. Although the FTICR platform is now broadly deployed as an integral component of many high-end proteomics-based research efforts, momentum is still building for the application of the platform towards nucleic acid-based analyses. In this work, we review fundamental aspects of nucleic acid analysis by FTICR, focusing primarily on the analysis of DNA oligonucleotides but also describing applications related to the characterization of RNA constructs. The goal of this review article is to give the reader a sense of the breadth and scope of the status quo of FTICR analysis of nucleic acids and to summarize a few recently published reports in which researchers have exploited the performance attributes of FTICR to characterize nucleic acids in support of basic and applied research disciplines including genotyping, drug discovery, and forensic analyses.

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Collision-activated dissociation (CAD) has been employed to assess the gas-phase fragmentation behavior of a series of 1:1 oligodeoxynucleotide (ODN):metal complexes over a range of charge states, using several ten-residue ODNs and a wide array of alkali, alkaline earth, and transition metals. For parent species in low to intermediate charge states, complexation with Ca(+2), Sr(+2), or Ba(+2) altered the relative intensity of M-B species, promoting loss of cytosine over loss of guanine. The relative intensities of sequence ions were largely unaffected. This behavior was most prevalent for isomeric sequences with complementary residues at the 5'- and 3'-termini, suggesting that metal complexation may change the gas-phase conformation and/or conformational dynamics for some sequences. In higher charge states, some ODN/Ba(+2) complexes produced abundant fragment ions corresponding to metallated a(n)(-m) species, which are not commonly observed in CAD mass spectra for deprotonated ODNs. The formation of these ions was most favored for complexes between Ba(+2) and ODN sequences with a thymine residue at Position 6. Literature precedent exists for the formation of a(n)(-m) ions from sequences in which covalent modification generates one or more neutral sites along the phosphate backbone. ODN/metal adducts in high charge states possess only a few acidic protons, and the juxtaposition of these neutral phosphate groups near thymine residues and the bound Ba(+2) ion may direct formation of the metallated a(n)(-m) species.

Potential adenine and minor groove binding platinum complexes

This paper is a focused review of our recent efforts to produce multi-nuclear platinum anti-cancer complexes that preferentially target adenine residues in DNA. Multi-nuclear platinum complexes, like cisplatin, predominantly form covalent adducts with guanine bases; however, controlling the pre-covalent binding association of the metal complex may modify this preference. NMR experiments, using oligonucleotides, indicate that multi-nuclear complexes linked by flexible diaminoalkanes will pre-associate in the DNA minor groove at A/T rich regions. Despite this pre-covalent binding preference, these complexes still predominantly covalently bind guanine residues. However, using 4,4'-dipyrazolylmethane (dpzm) as a linking ligand produces a dinuclear platinum complex, trans-[[PtCl(NH(3))(2)](2)mu-dpzm](2+), that covalently binds DNA with a preference for adenine bases. In vitro transcription assays also demonstrate that the dpzm-based complex covalently binds within an A/T rich region of the 512 base-pair segment of DNA used for the study.

Effect of the geometry of the central coordination sphere in antitumor trinuclear platinum complexes on DNA binding

Polynuclear platinum compounds comprise a unique class of anticancer agents with chemical and biological properties different from mononuclear platinum drugs. The lead compound of this class is bifunctional trinuclear platinum complex [[trans-PtCl(NH(3))(2)](2)mu-trans-Pt(NH(3))(2)[H(2)N(CH(2))(6)NH(2)](2)](4+) (1,0,1/t,t,t, BBR 3464). Interestingly, the geometry of the coordination spheres in this compound affects potency. For example, the central cis unit of [[trans-PtCl(NH(3))(2)](2)mu-cis-Pt(NH(3))(2)[H(2)N(CH(2))(6)NH(2)](2)](4+) (1,0,1/t,c,t, BBR 3499) results in substantially reduced cytotoxicity. It has been shown that the interactions of polynuclear platinum drugs with target DNA are distinct from the mononuclear-based cisplatin family. In the present work the DNA binding of 1,0,1/t,c,t in cell-free media was examined by the methods of molecular biophysics and compared to the binding of 1,0,1/t,t,t. The binding of 1,0,1/t,c,t is slower and less sequence specific. 1,0,1/t,c,t also forms on DNA long-range delocalized intrastrand and interstrand cross-links similarly as 1,0,1/t,t,t, although the frequency of interstrand adducts is markedly enhanced. Importantly, the adducts of 1,0,1/t,c,t distort DNA conformation and are repaired by cell-free extracts considerably more than the adducts of 1,0,1/t,t,t. It has been suggested that the unique properties of long-range interstrand cross-links of bifunctional trinuclear platinum complexes and resulting conformational alterations in DNA have critical consequences for their antitumor effects.

Phase II studies of BBR3464, a novel tri-nuclear platinum complex, in patients with gastric or gastro-oesophageal adenocarcinoma

BBR3464, a novel tri-nuclear platinum complex, forms long-range DNA adducts and is highly potent when compared with cisplatin in vitro. Preclinical studies demonstrated activity in cisplatin-resistant tumours and tumours with mutated p53 status. Phase I & II clinical studies gave preliminary indications of activity in melanoma, pancreatic, lung and ovarian cancers. The aim of this study was to determine the efficacy and confirm the toxicity of BBR3464 when given either as first- or second-line treatment for advanced disease in patients with gastric and gastro-oesphageal adenocarcinoma. Two multicentre, open label, Gehan design studies were conducted; one study used BBR3464 as first-line and the other as second-line treatment for metastatic or locally advanced disease. Nineteen first-line and 26 second-line patients were enrolled receiving a total of 74 and 53 infusions, respectively. Initially, seven patients in the second-line study received BBR3464 using the planned schedule of 1.1 mg/m2 every 4 weeks; however, 5 of these patients experienced dose-limiting grade 3 or 4 febrile neutropenia; subsequent patients in both studies were treated using the modified schedule of 0.9 mg/m2, every 21 days. In 1 of 17 evaluable, previously untreated patients, regression of multiple skin lesions was noted with stabilisation of lung metastases and maxillary sinus mass, lasting 155 days. In the first-line study, the median time to progression was 85 days [95% Confidence Interval (CI): 42, 127] (2.8 months) and in the second-line study, the median time to progression was 71 days [95% CI: 42, 109] and 38 days [95% CI: 32, 73] in the 1.1 and 0.9 mg/m2 dose level groups, respectively. Toxicity data were available for 45 patients. Neutropenia was the main toxicity seen (G3: 40%, G4: 40%). Febrile neutropenia was observed in six patients (15%) treated with 0.9 mg/m2 compared with five patients (71%) treated with 1.1 mg/m2 BBR3464. Other drug-related toxicities (G3/4) included: anaemia, thrombocytopenia, nausea, vomiting, diarrhoea, mucositis and fatigue. Diarrhoea and nausea/ vomiting were adequately controlled by the use of loperamide and antiemetics, respectively. Recruitment to the second-line study was closed early due to the poor response rate (1/17 evaluable, 6%; 95% CI: 1%, 27%) and short time to progression noted in the first-line study. Further studies with BBR3464 in this tumour type are not recommended.

Determination of a correction to improve mass measurement accuracy of isotopically unresolved polymerase chain reaction amplicons by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

The experimental determination of average mass by mass spectrometry is limited for large molecules due to the negative bias introduced by the natural distribution of isotopic abundances. This results in the measurement of the top-of-centroid (ToC) as opposed to the true centroid. We have developed a practical correction factor that is applied to the ToC measurement to largely remove the systematic bias introduced by nature. The correction factor is calculated easily using the average molecular mass (<100 kDa) of the analyte molecule and the full-width half maximum resolving power (<3,500) of the measurement. In addition, an approach to calculating resolving power is described that accurately predicts resolving power achievable for Fourier transform ion cyclotron resonance (FT-ICR) mass analysis of large molecules. A combination of internal calibration with a dual-electrospray source and application of the correction factor to average mass measurements improved the mass error from 192.5 to -35.0 ppm for a 44 kDa PCR amplicon.

Independent control of ion transmission in a jet disrupter dual-channel ion funnel electrospray ionization MS interface

A new atmospheric pressure ionization mass spectrometer (API-MS) interface has been developed to allow the control of ion transmission through the first vacuum stage of the mass spectrometer. The described interface uses a dual-heated capillary and a dual-inlet ion funnel design. Two electrosprays, aligned with the dual-capillary inlet, are used to introduce ions from different solutions independently into the MS. The initial design was specifically aimed at developing a method for the controlled introduction of calibrant ions in highly accurate mass measurements using Fourier transform ion cyclotron resonance mass spectrometer (FTICR). The dual-channel ion funnel has different inlet diameters that are aligned with the dual capillaries. The large diameter main channel of the ion funnel is used for analyte introduction to provide optimum ion transmission. The second, smaller diameter channel inlet includes a jet disrupter in the ion funnel to modulate the ion transmission through the channel. The two inlet channels converge into a single-channel ion funnel where ions from both channels are mixed, focused, and transmitted to the mass analyzer. Both theoretical simulations and experimental results show that the transmission of different m/z species in the small diameter channel of the ion funnel can be effectively modulated by varying the bias voltage on the jet disrupter. Both static and dynamic modulations of ion transmission are demonstrated experimentally by applying either a constant DC or a square waveform voltage to the jet disrupter. High ion transmission efficiency, similar to the standard single-channel ion funnel, is maintained in the main analyte channel inlet of the ion funnel over a broad m/z range with negligible "cross talk" between the two ion funnel inlet channels. Several possible applications of the new interface (e.g., for high-accuracy MS analysis of complex biological samples) are described.

Mass spectrometry of cis-diamminedichloroplatinum(II) adducts with the dinucleosidemonophosphates d(ApG), d(GpG) and d(TpC) in an ion trap

The detection and fragmentation behaviour of adducts of the chemotherapeutic cis-diamminedichloroplatinum(II) (cisplatin) with the dinucleosidemonophosphates d(ApG), d(GpG) and d(TpC) as model compounds for DNA adducts in an ion trap with electrospray ionization were studied. Mainly the monofunctional adduct, the bifunctional adduct and the bifunctional adduct with platinum bridging two dinucleosidemonophosphates were detected. In addition, several more complex adducts were seen resulting from reactions among these species. Adduct formation was low in the case of d(TpC). Fragmentation could be controlled strongly by varying the temperature of the transfer capillary; furthermore, tandem mass spectrometric (MS/MS) experiments on both the monofunctional and the bifunctional adducts were performed. For the adducts of d(ApG) and d(GpG) losses of NH(3) and HCl were the most dominant reactions, followed by the losses of one, then another two units of 98 amu from the sugar-phosphate backbone, whereas d(TpC)-Pt predominantly forms the dinucleosidemonophosphate. In the gas phase, the conversion of the monofunctional into the bifunctional adducts through binding to another site in the dinucleotide accompanied by loss of NH(3) or HCl could also be observed. The removal of a ligand from the coordination sphere of the square-planar platinum complexes appeared to be the crucial step for the induction of further fragmentation of the dinucleotide ligand. MS(n) experiments of the bifunctional adducts of d(ApG) and d(GpG) revealed different fragmentation pathways involving the loss of phosphoric acid, metaphosphoric acid, deoxyribose units (intact or dehydrated) and the nucleobases in different orders, leaving characteristic binding site-determining fragments. Fragmentation of these ions was also performed, mainly resulting in fragmentation of the bases. The study confirmed the remarkable stability of the platinum-guanine bond compared with other nucleobases.

Glutathione induces cellular resistance against cationic dinuclear platinum anticancer drugs

The sulfur-containing tripeptide glutathione (GSH) is one of the most abundant molecules in cells. Elevated levels of GSH render some types of cancer cells resistant against well-known platinum anti-cancer drugs such as cisplatin and carboplatin. Platinum complexes are often very reactive towards the cysteine residue of GSH, which detoxifies these compounds by a rapid binding mechanism. Clearly, this resistance mechanism poses a severe obstacle to any new platinum drugs designed to overcome cisplatin resistance. In the present study the cytotoxicity of dinuclear platinum compounds of the 1,1/t,t type, as developed by Farrell, is determined in human ovarium A2780 cells and in the cisplatin-resistant cell line A2780cisR, which possesses elevated levels of GSH. Further, the effect of depletion of GSH levels by L-buthionine-S,R-sulfoximine (L-BSO) in A2780cisR was investigated. The experiments show that detoxification by GSH is an effective resistance mechanism against dinuclear platinum compounds. However, the dinuclear complexes are less sensitive towards detoxification compared to cisplatin. This is probably because of the rapid binding of dinuclear cationic complexes to DNA. Compared to cisplatin, the rapid binding to DNA reduces the time during which the drug molecules are exposed to GSH in the cytosol. The reaction of a representative dinuclear compound with glutathione (pH 7, 37 degrees C) was studied in detail by 195Pt NMR. The dinuclear complex BBR3005 ([trans-PtCl(2)(NH(3))(2)(mu-H(2)N(CH(2))(6)NH(2))](2+), abbreviated as 1,1/t,t n=6), follows different pathways in the reaction with GSH, depending on the molar ratio of the reactants. When reacted in stoichiometric amounts (1:1), first a chloride on each platinum is replaced by a sulfur, forming a PtN(3)S product at -2977 ppm. After 2-3 h, this intermediate reacts further to form a sulfur-bridged N(3)Pt-S-PtN(3) species as the main product at -2811 ppm. When BBR3005 is reacted with GSH in a ratio of 1:4, the sulfur-bridged species is not observed. Instead, the final product is trans-Pt(GS)(2)(NH(3))(2) (at -3215 ppm); the same product appears if GSH is reacted with trans-PtCl(2)(NH(3))(2). Apparently, GSH first replaces the chlorides and subsequently degrades the dinuclear compound by replacement of the diaminealkyl linker.

Conformation, recognition by high mobility group domain proteins, and nucleotide excision repair of DNA intrastrand cross-links of novel antitumor trinuclear platinum complex BBR3464

The new antitumor trinuclear platinum compound [(trans-PtCl(NH(3))(2))(2)mu-trans-Pt(NH(3))(2)(H(2)N(CH(2))(6)NH(2))(2)](4+) (designated as BBR3464) is currently in phase II clinical trials. DNA is generally considered the major pharmacological target of platinum drugs. As such it is of considerable interest to understand the patterns of DNA damage. The bifunctional DNA binding of BBR3464 is characterized by the rapid formation of long range intra- and interstrand cross-links. We examined how the structures of the various types of the intrastrand cross-links of BBR3464 affect conformational properties of DNA, and how these adducts are recognized by high mobility group 1 protein and removed from DNA during in vitro nucleotide excision repair reactions. The results have revealed that intrastrand cross-links of BBR3464 create a local conformational distortion, but none of these cross-links results in a stable curvature. In addition, we have observed no recognition of these cross-links by high mobility group 1 proteins, but we have observed effective removal of these adducts from DNA by nucleotide excision repair. These results suggest that the processing of the intrastrand cross-links of BBR3464 in tumor cells sensitive to this drug may not be relevant to its antitumor effects. Hence, polynuclear platinum compounds apparently represent a novel class of platinum anticancer drugs acting by a different mechanism than cisplatin and its analogues.

Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post-genome era

The recent completion of the first rough draft of the human genome has provided fundamental information regarding our genetic make-up; however, the post-genome era will certainly require a host of new technologies to address complex biological questions. In particular, a rapid and accurate approach to characterize genetic markers, including short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is demanded. STRs are the most informative of the two polymorphisms owing to their remarkable variability and even dispersity throughout eukaryotic genomes. Mass spectrometry is rapidly becoming a significant method in DNA analysis and has high probability of revolutionizing the way in which scientists probe the human genome. It is our responsibility as biomolecular mass spectrometrists to understand the issues in genetic analysis and the capabilities of mass spectrometry so that we may fulfill our role in developing a rapid, reliable technology to answer specific biological questions. This perspective is intended to familiarize the mass spectrometry community with modern genomics and to report on the current state of mass spectrometry, specifically electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, for characterization of STRs.

Kinetic analysis of the stepwise formation of a long-range DNA interstrand cross-link by a dinuclear platinum antitumor complex: evidence for aquated intermediates and formation of both kinetically and thermodynamically controlled conformers

Reported here is a detailed study of the kinetics and mechanism of formation of a 1,4 GG interstrand cross-link by [(trans-PtCl(NH(3))(2))(2)(mu-NH(2)(CH(2))(n)NH(2))](2+) (1,1/t,t (n = 6), 1), the prototype of a novel class of platinum antitumor complexes. The reaction of the self-complementary 12-mer duplex 5'-[d(ATATGTACATAT)(2)] with (15)N-1 has been studied at 298 K, pH 5.4, by [(1)H,(15)N] HSQC 2D NMR spectroscopy. Initial electrostatic interactions with the duplex are observed for 1 and the monoaqua monochloro species (2). Aquation of 1 to yield 2 occurs with a pseudo-first-order rate constant of (4.15 +/- 0.04) x 10(-5) s(-1). 2 then undergoes monofunctional binding to the guanine N7 of the duplex to form 3 (G/Cl) with a rate constant of 0.47 +/- 0.06 M(-(1) s(-1). There is an electrostatic interaction between the unbound [PtN(3)Cl] group of 3 and the duplex, which is consistent with H-bonding interactions observed in the molecular model of the monofunctional (G/Cl) adduct. Closure of 3 to form the 1,4 GG interstrand cross-link (5) most likely proceeds via the aquated (G/H(2)O) intermediate (4) (pseudo-first-order rate constant = (3.62 +/- 0.04) x 10(-5) s(-1)) followed by closure of 4 to form 5 (rate constant = (2.7 +/- 1.5) x 10(-3) s(-1)). When closure is treated as direct from 3 (G/Cl) the rate constant is (3.39 +/- 0.04) x 10(-5) s(-1). Closure is ca. 10-55-fold faster than that found for 1,2 GG intrastrand cross-link formation by the diaqua form of cisplatin. Changes in the (1)H and (15)N shifts of the interstrand cross-link 5 indicate that the initially formed conformer (5(i)) converts irreversibly into other product conformer(s) 5(f). The NMR data for 5(i) are consistent with a molecular model of the 1,4 GG interstrand cross-link on B-form DNA, which shows that the NH(2) protons have no contacts except with solvent. The NMR data for 5(f) show several distinct NH(2) environments indicative of interactions between the NH(2) protons and the DNA. HPLC characterization of the final product showed only one major product peak that was confirmed by ESI-FTICR mass spectroscopy to be a cross-linked adduct of (15)N-1 and the duplex. The potential significance of these findings to the antitumor activity of dinuclear platinum complexes is discussed.

Homogeneous preparations of 3'-phosphoglycolate-terminated oligodeoxynucleotides from bleomycin-treated DNA as verified by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Single- and double-strand breaks bearing 3'-phosphoglycolate termini are among the most frequent lesions formed in DNA by ionizing radiation and other oxidative mutagens. In order to obtain homogeneous preparations of defined 3'-phosphoglycolate substrates for repair studies, 5'-(32)P-end-labeled partial duplex DNAs were treated with bleomycin, and individual cleavage products were isolated from polyacrylamide gels. The fragments were then treated with alkaline phosphatase and further purified by reverse-phase HPLC. Electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry of the purified oligomers produced molecular ions of the expected masses, with no detectable contaminants. Gas-phase sequencing by tandem mass spectrometry of these single species yielded the expected sequence ions and confirmed the presence of phosphoglycolate on the 3'-terminal fragments only. The fragments could be relabeled with polynucleotide kinase to yield highly purified, high-specific-activity substrates for repair studies.

Genotyping short tandem repeats using flow injection and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Characterizing polymerase chain reaction (PCR) amplicons has been accomplished for the first time using flow injection analysis coupled to electrospray ionization mass spectrometry (ESI-MS). The PCR amplicons were amplified at the human tyrosine hydroxylase short tandem repeat locus from an individual homozygotic for the 9.3 allele. One product was amplified using Pfu polymerase and yielded a blunt-ended amplicon of 82 base-pairs (bp) in length. The second PCR product was amplified using Taq polymerase that resulted in an amplicon with cohesive termini of 82 bp plus either mono- or diadenylation. The two PCR amplicons were alternatively injected using a 0.5-microL loop at 2 microM for the Pfu amplicon and 1 microM for the Taq amplicon with a flow rate of 200 nL/min during data acquisition. Both PCR amplicons were accurately identified using mass measurements illustrating the compatibility of ESI-MS for genotyping short tandem repeat sequences and the potential for high-throughput genotyping of large PCR amplicons.

A dual electrospray ionization source combined with hexapole accumulation to achieve high mass accuracy of biopolymers in Fourier transform ion cyclotron resonance mass spectrometry

A dual electrospray ionization (ESI) source employed with hexapole accumulation and gated trapping provides a novel method of using an internal standard to achieve high mass accuracies in Fourier transform ion cyclotron resonance mass spectrometry. Two ESI emitters are sequentially positioned in front of the heated metal capillary inlet by a solenoid fitted to an XYZ micromanipulator; one emitter contains the analyte(s) of interest and the other an internal standard. A 5 V transistor-transistor logic pulse from the data station controls the solenoid by means of a solid-state relay so that matching of spectral peak intensities (i.e., analyte and internal standard intensities) can be accomplished by adjusting the hexapole accumulation time for each species. Polythymidine, d(pT)18, was used as the internal standard for all studies reported here. The absolute average error for an internally calibrated 15-mer oligonucleotide (theoretical monoisotopic mass = 4548.769 Da) was -1.1 ppm (external calibration: 41 ppm) with a standard deviation of +/-3.0 ppm (external calibration: +/-24 ppm) for a total of 25 spectra obtained at various hexapole accumulation time ratios. Linear least squares regression analysis was carried out and revealed a linear dependence of the magnitudes of the peak height ratios (analyte/internal standard) vs. hexapole accumulation time ratios (analyte/internal standard) which is described by the following equation: y = 0.45 x - 0.02. The fitted line had a %RSD of the slope of 28% with an R2 of 0.93. The applicability of this methodology was extended to a polymerase chain reaction product with a theoretical average molecular mass of 50,849.20 Da. With the internal standard, d(pT)18, an absolute average error of -8.9 ppm (external calibration: 44 ppm) based on five measurements was achieved with a standard deviation of 11 ppm (external calibration: +/-36 ppm), thus illustrating this method's use for characterizing large biomolecules such as those encountered in genomics and proteomics related research.