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.
This review summarizes clinical and pre-clinical results on platinum anti-cancer drug formulations. A concise summary of the use of oxidation state to modulate cancer pharmacology is given for Pt(IV) ...complexes, distinct from the clinically used Pt(II) drugs. The chemistry of platinum drug formulation combines aspects of kinetics of active moiety release from nominally weak-binding ligands (bond cleavage from platinum-carboxylate and platinum-phosphate) in polymers and nanoparticles with pharmacological considerations of plasma distribution and cellular accumulation. The action of any molecular entity as a drug is influenced by its ADME profile--absorption, distribution, metabolism and excretion. The purpose of drug formulation is to alter any or all of these parameters with the ultimate goal of improving the efficacy and reducing side effects with the possibility to target drugs directly to the tumor site. The diverse array of approaches includes liposomes, polymers (not limited to peptides, dendrimers, biodegradable polymers, polysaccharides, and metallic nanoparticles). Functionalization of the surfaces of nanoparticles with antibodies or cellular surface recognition motifs may further target specific cancers.
RNA triplexes are significant tertiary structure motifs that are found in many functional RNAs. Hence, small molecules capable of recognition, binding, and stabilization of the triple-helical RNA ...structures are emerging as attractive potential molecular biology tools and therapeutic agents. Here, we utilize methods of molecular biology and biophysics to study the interactions of a series of antitumor substitution-inert polynuclear platinum complexes (SI-PPCs) with triple-helical RNA structures. We show that SI-PPCs recognize and stabilize RNA triplexes and inhibit reverse transcription preferentially in the RNA template prone to the triplex formation. These so far unexplored properties of SI-PPCs suggest that the targeting of triple-stranded regions in RNA might contribute to the biological effects of SI-PPCs.
The noncovalent analogues of antitumor polynuclear platinum complexes represent a structurally discrete class of platinum drugs. Their chemical and biological properties differ significantly from ...those of most platinum chemotherapeutics, which bind to DNA in a covalent manner by formation of Pt-DNA adducts. In spite of the fact that these noncovalent polynuclear platinum complexes contain no leaving groups, they have been shown to bind to DNA with high affinity. We report here on the DNA condensation properties of a series of noncovalent analogues of antitumor polynuclear platinum complexes described by biophysical and biochemical methods. The results demonstrate that these polynuclear platinum compounds are capable of inducing DNA condensation at more than 1 order of magnitude lower concentrations than conventional spermine. Atomic force microscopy studies of DNA condensation confined to a mica substrate have revealed that the DNA morphologies become more compact with increasing concentration of the platinum complexes. Moreover, we also found that the noncovalent polynuclear platinum complex {Pt(NH3)3}2-μ-{trans-Pt(NH3)2(NH2(CH2)6NH2)2}(6+) (TriplatinNC-A) binds to DNA in a sequence-dependent manner, namely, to A/T-rich sequences and A-tract regions, and that noncovalent polynuclear platinum complexes protect DNA from enzymatic cleavage by DNase I. The results suggest that mechanisms of antitumor and cytotoxic activities of these complexes may be associated with their unique ability to condense DNA along with their sequence-specific DNA binding. Owing to their high cellular accumulation, it is also reasonable to suggest that their mechanism of action is based on the competition with naturally occurring DNA condensing agents, such as polyamines spermine, spermidine, and putrescine, for intracellular binding sites, resulting in the disturbance of the correct binding of regulatory proteins initiating the onset of apoptosis.
The formation of triple‐helical DNA is implicated in the regulation of gene expression. The triplexes are, however, unstable under physiological conditions so that effective stabilizers for the ...triplex formation are needed. Herein, we describe a new strategy for the stabilization of such triplexes that is based on antitumor substitution‐inert polynuclear platinum complexes (SI‐PPCs). These compounds were previously shown to bind to DNA through the phosphate clamp—a discrete mode of DNA–ligand recognition distinct from the canonical intercalation and minor‐groove binding. We have found that SI‐PPCs efficiently inhibit DNA synthesis by DNA polymerase in sequences prone to the formation of pyrimidine‐ and purine‐motif triplex DNAs. Moreover, the results suggest that SI‐PPCs are able to induce the formation of triple‐helical DNA between duplexes and strands that are not completely complementary to each other. Collectively, these data provide evidence that SI‐PPCs are very efficient stabilizers of triple‐stranded DNA that might exert their action by stabilizing higher‐order structures such as triple‐helical DNA.
Stable enough: Substitution‐inert trinuclear platinum complexes efficiently inhibit DNA synthesis by DNA polymerase in sequences prone to the formation of pyrimidine‐ and purine‐motif triplex DNAs. The data suggest that these compounds are very efficient stabilizers of triple‐stranded DNA.
Compounds condensing DNA and RNA molecules can essentially affect important biological processes including DNA replication and transcription. Here, this work shows with the aid of total intensity ...light scattering, gel electrophoresis, and atomic force microscopy (AFM) that the substitution‐inert polynuclear platinum complexes (SI‐PPCs), particularly {trans‐Pt(NH3)2(NH2(CH2)6‐ NH3+)}2‐μ‐{trans‐Pt(NH3)2(NH2(CH2)6NH2)2}8+ (Triplatin NC), exhibit an unprecedented high potency to condense/aggregate fragments of DNA and RNA as short as 20 base pairs. SI‐PPCs condensates are distinctive from those generated by the naturally occurring polyamines (commonly used DNA compacting/condensing agents). Collectively, the results further confirm that SI‐PPCs are very efficient inducers of condensation of DNA and RNA, including their short fragments that might have potential in gene therapy, biotechnology, and bionanotechnology. Moreover, the data confirm the structural advantages of the phosphate clamp, with a well‐defined rigid DNA recognition motif in initiating condensation and aggregation phenomena on oligonucleotides.
Substitution inert trinuclear platinum complexes are very efficient inducers of condensation of DNA and RNA, including their short fragments that might have potential in gene therapy, biotechnology, and bionanotechnology.
The trinuclear platinum complexes (TriplatinNC‐A {Pt(NH3)3}2‐μ‐{trans‐Pt(NH3)2(NH2(CH2)6NH2)2}6+, and TriplatinNC {trans‐Pt(NH3)2(NH2(CH2)6NH3+)}2‐μ‐{trans‐Pt(NH3)2(NH2(CH2)6NH2)2}8+) are ...biologically active agents that bind to DNA through noncovalent (hydrogen bonding, electrostatic) interactions. Herein, we show that TriplatinNC condenses DNA with a much higher potency than conventional DNA condensing agents. Both complexes induce aggregation of small transfer RNA molecules, and TriplatinNC in particular completely inhibits DNA transcription at lower concentrations than naturally occurring spermine. Topoisomerase I‐mediated relaxation of supercoiled DNA was inhibited by TriplatinNC‐A and TriplatinNC at concentrations which were 60 times and 250 times lower than that of spermine. The mechanisms for the biological activity of TriplatinNC‐A and TriplatinNC may be associated with their ability to condense/aggregate nucleic acids with consequent inhibitory effects on crucial enzymatic activities.
Pt bridges the gap: A general mechanism showing the biological effects of trinuclear platinum complexes, which bind to DNA through noncovalent interactions, may be associated with their unique ability to efficiently condense or aggregate nucleic acids with consequent inhibitory effects on crucial enzymatic activities. Scale bars in picture=500 nm.
Towards Antitumor Active trans-Platinum Compounds Aris, Sheena M.; Farrell, Nicholas P.
European Journal of Inorganic Chemistry,
April 2009, Letnik:
2009, Številka:
10
Book Review, Journal Article
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.
Limitations of clinical platinum(II) therapeutics include systemic toxicity and inherent resistance. Modern approaches, therefore, seek new ways to deliver active platinum(II) to discrete nucleic ...acid targets. In the field of antigene therapy, triplex‐forming oligonucleotides (TFOs) have attracted interest for their ability to specifically recognise extended duplex DNA targets. Here, we report a click chemistry based approach that combines alkyne‐modified TFOs with azide‐bearing cis‐platinum(II) complexes—based on cisplatin, oxaliplatin, and carboplatin motifs—to generate a library of PtII‐TFO hybrids. These constructs can be assembled modularly and enable directed platinum(II) crosslinking to purine nucleobases on the target sequence under the guidance of the TFO. By covalently incorporating modifications of thiazole orange—a known DNA‐intercalating fluorophore—into PtII‐TFOs constructs, enhanced target binding and discrimination between target and off‐target sequences was achieved.
Nucleic acid click chemistry has been used for the development of cis‐platinum(II)/triplex‐forming oligonucleotide hybrid biomaterials. This modular approach allows the incorporation of cis‐platinum(II) at practically any location within the probe strand. These hybrid biomaterials display discrete and efficient crosslinking of purine‐rich genetic elements of the GFP gene.
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