Comparison of Mass Spectrometry and Other Techniques for Probing Interactions Between Metal Complexes and DNA

Metal-Based Drug-DNA Interactions and Analytical Determination Methods

DNA structure has many potential places where endogenous compounds and xenobiotics can bind. Therefore, xenobiotics bind along the sites of the nucleic acid with the aim of changing its structure, its genetic message, and, implicitly, its functions. Currently, there are several mechanisms known to be involved in DNA binding. These mechanisms are covalent and non-covalent interactions. The covalent interaction or metal base coordination is an irreversible binding and it is represented by an intra-/interstrand cross-link. The non-covalent interaction is generally a reversible binding and it is represented by intercalation between DNA base pairs, insertion, major and/or minor groove binding, and electrostatic interactions with the sugar phosphate DNA backbone. In the present review, we focus on the types of DNA-metal complex interactions (including some representative examples) and on presenting the methods currently used to study them.

Effect of substituents on the ability of nickel Schiff base complexes with four pendant groups to bind to G-quadruplexes

The synthesis of eleven new nickel Schiff base complexes each bearing four pendant groups is reported. The structures of the complexes differ in the identity of the pendant groups and/or diamine moiety. All complexes were characterised by microanalysis, Nuclear Magnetic Resonance (NMR) spectroscopy and Electrospray Ionisation Mass Spectrometry (ESI-MS), while the solid-state structures of two of the molecules were also determined using X-ray crystallographic methods. The DNA binding properties of the nickel complexes with double stranded DNA and a range of G-quadruplex DNA structures was explored using different spectroscopic methods as well as computational techniques. Results from ESI-MS experiments and Fluorescent Indicator Displacement (FID) assays were consistent with each other and indicated that varying the diamine moiety had less influence on DNA affinity than changing the pendant groups. These conclusions were also generally supported by results obtained from UV melting experiments and Fluorescence Resonance Energy Transfer (FRET) assays. The cytotoxicity of selected examples of the new complexes, and close analogues reported recently, towards V79 Chinese hamster lung cancer cells and THP-1 human leukemia cells was measured. All were found to display modest cytotoxicity, with flow cytometry experiments suggesting an apoptotic pathway was the most likely mechanism of cell death.

A biophysical study of the interactions of palladium(II), platinum(II) and gold(III) complexes of aminopyridyl-2,2'-bipyridine ligands with RNAs and other nucleic acid structures

Metal compounds form an attractive class of ligands for a variety of nucleic acids. Five metal complexes bearing aminopyridyl-2,2'-bipyridine tetradentate ligands and possessing a quasi-planar geometry were challenged toward different types of nucleic acid molecules including RNA polynucleotides in the duplex or triplex form, an RNA Holliday four-way junction, natural double helix DNA and a DNA G-quadruplex. The binding process was monitored comparatively using different spectroscopic and melting methods. The binding preferences that emerge from our analysis are discussed in relation to the structural features of the metal complexes.

The effect of isomerism and other structural variations on the G-quadruplex DNA-binding properties of some nickel Schiff base complexes

A series of novel isomeric nickel Schiff base complexes, as well as nickel complexes of related ligands having asymmetric structures have been prepared and characterised using microanalysis, 1H and 13C NMR spectroscopy and ESI-MS. The Schiff base ligands were prepared by condensation reactions involving ethylenediamine and different derivatives of benzophenone. The solid-state structures of eight of the complexes were also determined and revealed that each possessed a regular square planar coordination geometry around the metal ion. Many of the new complexes featured at least one, and in many instances two, protonatable pendant groups that enhance aqueous solubility. This enabled the DNA binding properties of the latter complexes to be explored using a variety of instrumental approaches, including ESI-MS, circular dichroism (CD) spectroscopy, FRET melting assays and FID assays, as well as molecular docking studies. The results of experiments performed using ESI-MS suggested that none of the nickel complexes exhibit a high affinity towards either a double stranded DNA (dsDNA) molecule D2, or the parallel unimolecular quadruplex DNA (qDNA) molecule Q1. In contrast, complexes (8) and (12) both gave spectra which reflected a significant level of binding to the parallel tetramolecular qDNA Q4. The results of binding experiments performed using CD spectroscopy suggested that (12) exhibits a significant level of affinity towards most types of DNA, while (4) shows a preference for interacting with parallel, unimolecular qDNA molecules. Complex (4) produced the lowest values of DC50 in FID assays performed using parallel Q1 or Q4, confirming its affinity for these qDNA molecules. The results of FRET melting experiments provided further evidence that (12), along with (8), can interact extensively with anti-parallel unimolecular qDNA. Experiments which monitored the effect of the nickel complexes on the melting temperature of D2 showed that none had a stabilising effect on this dsDNA molecule.

A new class of quadruplex DNA-binding nickel Schiff base complexes

A new nickel Schiff base complex shows selective binding behaviour towards quadruplex DNA and cytotoxicity against cancer cells.

Molecular methods for assessment of non-covalent metallodrug-DNA interactions

The binding of small molecule metallodrugs to discrete regions of nucleic acids is an important branch of medicinal chemistry and the nature of these interactions, allied with sequence selectivity, forms part of the backbone of modern medicinal inorganic chemistry research. In this tutorial review we describe a range of molecular methods currently employed within our laboratories to explore novel metallodrug-DNA interactions. At the outset, an introduction to DNA from a structural perspective is provided along with descriptions of non-covalent DNA recognition focusing on intercalation, insertion, and phosphate binding. Molecular methods, described from a non-expert perspective, to identify non-covalent and pre-associative nucleic acid recognition are then demonstrated using a variety of techniques including direct (non-optical) and indirect (optical) methods. Direct methods include: X-ray crystallography; NMR spectroscopy; mass spectrometry; and viscosity while indirect approaches detail: competitive inhibition experiments; fluorescence and absorbance spectroscopy; circular dichroism; and electrophoresis-based techniques. For each method described we provide an overview of the technique, a detailed examination of results obtained and relevant follow-on of advanced biophysical/analytical techniques. To achieve this, a selection of relevant copper(ii) and platinum(ii) complexes developed within our laboratories are discussed and are compared, where possible, to classical DNA binding agents. Applying these molecular methods enables us to determine structure-activity factors important to rational metallodrug design. In many cases, combinations of molecular methods are required to comprehensively elucidate new metallodrug-DNA interactions and, from a drug discovery perspective, coupling this data with cellular responses helps to inform understanding of how metallodrug-DNA binding interactions manifest cytotoxic action.

Effect of structure variations on the quadruplex DNA binding ability of nickel Schiff base complexes

The synthesis of two new series of nickel complexes is described, along with their ability to bind to duplex and quadruplex DNA structures.

Anti-proliferative activity and DNA/BSA interactions of five mono- or di-organotin(iv) compounds derived from 2-hydroxy-N′-[(2-hydroxy-3-methoxyphenyl)methylidene]-benzohydrazone

Five hydrazone Schiff base organotin(iv) complexes were synthesized and their anticancer mechanism was preliminarily studied.

Synthesis and characterisation of nickel Schiff base complexes containing the meso-1,2-diphenylethylenediamine moiety: selective interactions with a tetramolecular DNA quadruplex

Two nickel(ii) Schiff base complexes exhibit binding selectivity for a tetramolecular DNA quadruplex.

Organotin(IV) complexes derived from Schiff base N'-[(1E)-(2-hydroxy-3-methoxyphenyl)methylidene]pyridine-4-carbohydrazone: synthesis, in vitro cytotoxicities and DNA/BSA interaction

Five organotin(IV) compounds were synthesized from N'-[(1E)-(2-hydroxy-3-methoxyphenyl)methylidene]pyridine-4-carbohydrazone and the corresponding dialkyltin(IV) or trialkyltin(IV) precursor. Solid state structures were determined by IR, elemental analysis, NMR spectroscopy, and for 1, 2, 4 and 5 single crystal X-ray diffraction analysis. Compounds 1, 2 and 4 are monomers with the tin atoms five-coordinated in distorted trigonal bipyramid, of which the deprotonated Schiff base ligand chelate to tin center in the enolic tridentate mode. Differently, in compound 5, the enolization does not occur for the Schiff base ligand, and only the pyridinyl N atom and the deprotonated phenol hydroxyl oxygen atom participate in the coordination. Fascinatingly, six trimethyltin(IV) coordination units are linked by the Sn⋯N weak interaction atoms and form a 72-membered crown-like macrocycle. Preliminary in vitro cytotoxicity studies on five human tumor cells lines (HL-60, A549, HT-29, HCT-116 and Caco-2) by MTT assay reveal that di-n-butyltin(IV) complex 2 and diphenyltin(IV) complex 4 triggered significant antiproliferative effects in cultured tumor cells, and their cytotoxic activity correlates with intracellular organotin(IV) concentration. The interaction of the complexes with calf thymus DNA (CT-DNA) has been explored by absorption and emission titration methods, which revealed that complexes 2 and 4 interact with CT-DNA through groove-binding and partial intercalation of the extended planar ligand with the DNA base stack. Further, the albumin interactions of complexes 2 and 4 were investigated using fluorescence quenching spectra and synchronous fluorescence spectra. Studies reveal that di-n-butyltin(IV) complex 2 with higher cytotoxicity show stronger DNA/BSA interaction than diphenyltin(IV) complex 4.

Does cytotoxicity of metallointercalators correlate with cellular uptake or DNA affinity?

The cytotoxicity of the metallointercalators, [Pt(5,6-dimethyl-1,10-phenanthroline)(trans-1R,2R-diaminocyclohexane)](2+) ([56MERR]) and [Pt(5,6-dimethyl-1,10-phenanthroline)(trans-1S,2S-diaminocyclohexane)](2+) ([56MESS]), towards A549 human lung cancer cells was examined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The IC(50) value obtained following exposure of A549 cells to [56MESS] for 4 h was approximately three times smaller than that obtained when [56MERR] was administered under the same conditions, indicating that the former complex displayed greater cytotoxicity. Both IC(50) values were greater than that obtained after exposure of A549 cells to cisplatin, demonstrating that the latter compound was the most cytotoxic of the three examined. Microprobe synchrotron radiation X-ray fluorescence (SR-XRF) analyses of metallointercalator-treated A549 cells showed that platinum became localised in DNA-rich regions of the nucleus. In contrast, when the same cells were treated with cisplatin the metal became distributed throughout the cell. Determination of the maximum concentration of platinum present inside the cells using graphite furnace atomic absorption spectrophotometry (GFAAS) of platinum-treated cells suggested that there was greater uptake of [56MERR] compared to [56MESS] by the A549 cells, and that platinum uptake did not account for the greater toxicity of [56MESS], as assessed by the MTT assay. Electrospray ionization mass spectrometric (ESI-MS) and circular dichroism (CD) spectroscopic studies of solutions containing either [56MERR] or [56MESS], and a duplex hexadecamer molecule, showed the two metallointercalators displayed very similar affinity towards the nucleic acid. Overall these results indicate that the difference in cytotoxicity of the two platinum metallointercalators is probably the result of variations in their interactions with other cellular components.

Developments in Electrospray Ionization Mass Spectrometry of Non-Covalent DNA–Ligand Complexes

Many anti-cancer drugs function by binding non-covalently to double-stranded (ds) DNA. Electrospray ionization mass spectrometry (ESI-MS) has emerged over the past decade as a sensitive technique for the determination of stoichiometries and relative binding affinities of DNA–ligand interactions. The chromosome contains nucleotide sequences, for example, guanosine-rich regions, that predispose them to the formation of higher order structures such as quadruplex DNA (qDNA). Sequences that form qDNA are found in the telomeres. The proposal that ligands that stabilize qDNA might interfere with the activity of telomerase in cancer cells has stimulated the search for ligands that are selective for qDNA over dsDNA. The insights gained from the development of ESI-MS methods for analysis of non-covalent dsDNA–ligand complexes are now being applied in the search for qDNA-selective ligands. ESI-MS is a useful first-pass screening technique for qDNA-binding ligands. This short review describes some experimental considerations for ESI-MS analysis of DNA–ligand complexes, briefly addresses the question of whether non-covalent DNA–ligand complexes are faithfully transferred from solution to the gas phase, discusses ion mobility mass spectrometry as a technique for probing this issue, and highlights some recent ESI-MS studies of qDNA-selective ligands.

A mass spectrometric investigation of the ability of metal complexes to modulate transcription factor activity

ESI mass spectrometry was used to assess the ability of metal complexes to inhibit binding of a transcription factor to a DNA molecule containing its recognition sequence.

Oligopyridine-ruthenium(II)-amino acid conjugates: synthesis, characterization, DNA binding properties and interactions with the oligonucleotide duplex d(5'-CGCGCG-3')2

Diastereomeric oligopyridine-ruthenium(II)-amino acid conjugated complexes of the general formulas Lambda- and Delta-[Ru(bpy)(2)(4,4'(CO(2)Y)(2)-bpy)](2+), where Y = L-AlaCONH(2), L-LysCONH(2), L-HisCONH(2), L-TyrCONH(2)), were synthesized and characterized. Their binding properties with ct-DNA and the oligonucleotide duplex d(5'CGCGCG-3')(2), by means of circular dichroism (CD), NMR spectroscopy and DNA thermal denaturation (T(m)) curves were studied. CD and T(m) data indicate that all diastereomeric complexes bind to the DNA major groove, Delta-diastereomers in a similar manner, while Lambda-diastereomers in dependence of the nature of the amino acid. NMR studies of d(5'CGCGCG-3')(2), and the complexes Delta-1, Delta-2, Lambda-1 and Lambda-2 indicate that Delta-1 and Delta-2 were bound having the ancillary bpy ligands towards the DNA groove, while the corresponding Lambda-1 and Lambda-2 were orientated in a similar way, facing the ligand 4,4'(CO(2)Y)(2)bpy towards the DNA major groove. Photoinduced DNA cleavage was observed in all cases studied, which take place through singlet oxygen production. Delta-4 and Lambda-4 show the lower photoinduced cleavage yield, probably because the singlet oxygen ((1)O(2)) oxidizes not only the DNA phosporodiesteric bonds but the tyrosine's phenolic OH bond as well.

Evaluation of binding selectivities and affinities of platinum-based quadruplex interactive complexes by electrospray ionization mass spectrometry

The quadruplex binding affinities and selectivities of two large pi-surface Pt(II) phenanthroimidazole complexes, as well as a smaller pi-surface platinum bipyridine complex and a larger Ru(II) complex, were evaluated by electrospray ionization mass spectrometry. Circular dichroism (CD) spectroscopy was used to determine the structures of various quadruplexes and to study the thermal denaturation of the quadruplexes in the absence and presence of the metal complexes. In addition, chemical probe reactions with glyoxal were used to monitor the changes in the quadruplex conformation because of association with the complexes. The platinum phenanthroimidazole complexes show increased affinity for several of the quadruplexes with elongated loops between guanine repeats. Quadruplexes with shorter loops exhibited insubstantial binding to the transition metal complexes. Similarly binding to duplex and single strand oligonucleotides was low overall. Although the ruthenium-based metal complex showed somewhat enhanced quadruplex binding, the Pt(II) complexes had higher quadruplex affinities and selectivities that are attributed to their square planar geometries. The chemical probe reactions using glyoxal indicated increased reactivity when the platinum phenanthroimidazole complexes were bound to the quadruplexes, thus suggesting a conformational change that alters guanine accessibility.