G‐Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy

A curated library of circular dichroism spectra of 23 G‐quadruplexes of known structure was built and analyzed. The goal of this study was to use this reference library to develop an algorithm to derive quantitative estimates of the secondary structure content of quadruplexes from their experimental CD spectra. Principal component analysis and singular value decomposition were used to characterize the reference spectral library. CD spectra were successfully fit to obtain estimates of the amounts of base steps in anti–anti, syn–anti or anti–syn conformations, in diagonal or lateral loops, or in other conformations. The results show that CD spectra of nucleic acids can be analyzed to obtain quantitative structural information about secondary structure content in an analogous way to methods used to analyze protein CD spectra.     

A Redox‐Activated G‐Quadruplex DNA Binder Based on a Platinum(IV)–Salphen Complex

There has been increasing interest in the development of small molecules that can selectively bind to G‐quadruplex DNA structures. The latter have been associated with a number of key biological processes and therefore are proposed to be potential targets for drug development. Herein, we report the first example of a reduction‐activated G‐quadruplex DNA binder. We show that a new octahedral platinum(IV)–salphen complex does not interact with DNA in aqueous media at pH 7.4; however, upon addition of bioreductants such as ascorbic acid or glutathione, the compound is readily reduced to the corresponding square planar platinum(II) complex. In contrast to the parent platinum(IV) complex, the in situ generated platinum(II) complex has good affinity for G‐quadruplex DNA.     

A Nitroxide‐Tagged Platinum(II) Complex Enables the Identification of a DNA G‐Quadruplex Binding Mode

We reported a novel strategy for investigating small molecule binding to G‐quadruplexes (GQs). A newly synthesized dinuclear platinum(II) complex (Pt₂L) containing a nitroxide radical was shown to selectively bind a GQ‐forming sequence derived from human telomere (hTel). Using the nitroxide moiety as a spin label, electron paramagnetic resonance (EPR) spectroscopy was carried out to investigate binding between Pt₂L and hTel GQ. Measurements indicated that two molecules of Pt₂L bind with one molecule of hTel GQ. The inter‐spin distance measured between the two bound Pt₂L, together with molecular docking analyses, revealed that Pt₂L predominately binds to the neighboring narrow and wide grooves of the G‐tetrads as hTel adopts the antiparallel conformation. The design and synthesis of nitroxide tagged GQ binders, and the use of spin‐labeling/EPR to investigate their interactions with GQs, will aid the development of small molecules for manipulating GQs involved in crucial biological processes.     

Dinuclear Ruthenium(II) Complexes That Induce and Stabilise G‐Quadruplex DNA

A series of dinuclear ruthenium(II) complexes were synthesised, and the complexes were determined to be new highly selective compounds for binding to telomeric G‐quadruplex DNA. The interactions of these complexes with telomeric G‐quadruplex DNA were studied by using circular dichroism (CD) spectroscopy, fluorescence resonance energy transfer (FRET) melting assays, isothermal titration calorimetry (ITC) and molecular modelling. The results showed that the complexes 1 , 2 and 4 induced and stabilised the formation of antiparallel G‐quadruplexes of telomeric DNA in the absence of salt or in the presence of 100 mM K⁺‐containing buffer. Furthermore, complexes 1 and 2 strongly bind to and effectively stabilise the telomeric G‐quadruplex structure and have significant selectivity for G‐quadruplex over duplex DNA. In comparison, complex 3 had a much lesser effect on the G‐quadruplex, suggesting that possession of a suitably sized plane for good π–π stacking with the G‐quadruplets is essential for the interaction of the dinuclear ruthenium(II) complexes with the G‐quadruplex. Moreover, telomerase inhibition by the four complexes and their cellular effects were studied, and complex 1 was determined to be the most promising inhibitor of both telomerase and HeLa cell proliferation.     

Assembly of Palladium(II) and Platinum(II) Metallo‐Rectangles with a Guanosine‐Substituted Terpyridine and Study of Their Interactions with Quadruplex DNA

Two novel [2+2] metallo‐assemblies based on a guanosine‐substituted terpyridine ligand ( 1 ) coordinated to palladium(II) ( 2 a ) and platinum(II) ( 2 b ) are reported. These supramolecular assemblies have been fully characterized by NMR spectroscopy, ESI mass spectrometry and elemental analyses. The palladium(II) complex ( 2 a ) has also been characterized by single crystal X‐ray diffraction studies confirming that the system is a [2+2] metallo‐rectangle in the solid state. The stabilities of these [2+2] assemblies in solution have been confirmed by DOSY studies as well as by variable temperature ¹H NMR spectroscopy. The ability of these dinuclear complexes to interact with quadruplex and duplex DNA was investigated by fluorescent intercalator displacement (FID) assays, fluorescence resonance energy transfer (FRET) melting studies, and electrospray mass spectrometry (ESI‐MS). These studies have shown that both these assemblies interact selectively with quadruplex DNA (human telomeric DNA and the G‐rich promoter region of c‐myc oncogene) over duplex DNA, and are able to induce dimerization of parallel G‐quadruplex structures.     

Honeycomb‐like Ordered Assembly of DNA Induced by Flexible Binuclear Ruthenium(II)–Polypyridyl Complexes

A series of binuclear ruthenium(II)–polypyridyl complexes of the type [Ru₂(N‐N)₄(BPIMBp)]⁴⁺, in which N‐N is 2,2′‐bipyridine (bpy; 1 ), 1,10‐phenanthroline (phen; 2 ), dipyrido[3,2‐d:2′,3‐f] quinoxaline (dpq; 3 ), dipyrido[3,2‐a:2′,3′‐c] phenanzine (dppz; 4 ), and 1,4′‐bis[(2‐pyridin‐2‐yl)‐1H‐imidazol‐1‐yl)methyl]‐1,1′‐biphenyl (BPIMBp) is a bridging ligand, have been synthesized and characterized. These complexes are charged (4+) cations and flexible due to the ?CH₂ group of the bridging ligand and possess terminal ligands with variable intercalative abilities. The interaction of complexes 1 – 4 with calf thymus DNA (CT‐DNA) was explored by using UV/Vis absorption spectroscopy, steady‐state emission, emission quenching with K₄[Fe(CN)₆], ethidium bromide displacement assay, Hoechst displacement assay, and viscosity measurements and revealed a groove‐binding mode for all the complexes through a spacer and an intercalative mode for complexes 3 and 4 . A decrease in the viscosity of DNA revealed bending and coiling of DNA, an initial step toward aggregation. Interestingly, a distinctive honeycomb‐like ordered assembly of the DNA–complex species was visualized by fluorescence microscopy in the solution state. The use of SEM and AFM confirmed the disordered self‐organization of the DNA–complex adduct on evaporation of the solvent. The small orderly nanosized DNA aggregates were confirmed by means of circular dichroism, dynamic light scattering (DLS), and TEM. These complexes are moderately cytotoxic against three different cell lines, namely, MCF‐7, HeLa, and HL‐60.     

Structure‐Based Design of Platinum(II) Complexes as c‐myc Oncogene Down‐Regulators and Luminescent Probes for G‐Quadruplex DNA

A series of platinum(II) complexes with tridentate ligands was synthesized and their interactions with G‐quadruplex DNA within the c‐myc gene promoter were evaluated. Complex 1 , which has a flat planar 2,6‐bis(benzimidazol‐2‐yl)pyridine (bzimpy) scaffold, was found to stabilize the c‐myc G‐quadruplex structure in a cell‐free system. An in silico G‐quadruplex DNA model has been constructed for structure‐based virtual screening to develop new Pt^II‐based complexes with superior inhibitory activities. By using complex 1 as the initial structure for hit‐to‐lead optimization, bzimpy and related 2,6‐bis(pyrazol‐3‐yl)pyridine (dPzPy) scaffolds containing amine side‐chains emerge as the top candidates. Six of the top‐scoring complexes were synthesized and their interactions with c‐myc G‐quadruplex DNA have been investigated. The results revealed that all of the complexes have the ability to stabilize the c‐myc G‐quadruplex. Complex 3 a ([Pt^II L2R ] ⁺ ; L2 =2,6‐bis[1‐(3‐piperidinepropyl)‐1H‐enzo[d]imidazol‐2‐yl]pyridine, R =Cl) displayed the strongest inhibition in a cell‐free system (IC₅₀=2.2 μM ) and was 3.3‐fold more potent than that of 1 . Complexes 3 a and 4 a ([Pt^II L3R ]⁺; L3 =2,6‐bis[1‐(3‐morpholinopropyl)‐1H‐pyrazol‐3‐yl]pyridine, R =Cl) were found to effectively inhibit c‐myc gene expression in human hepatocarcinoma cells with IC₅₀ values of ≈17 μM , whereas initial hit 1 displayed no significant effect on gene expression at concentrations up to 50 μM . Complexes 3 a and 4 a have a strong preference for G‐quadruplex DNA over duplex DNA, as revealed by competition dialysis experiments and absorption titration; 3 a and 4 a bind G‐quadruplex DNA with binding constants (K) of approximately 10⁶–10⁷ dm³ mol^?1, which are at least an order of magnitude higher than the K values for duplex DNA. NMR spectroscopic titration experiments and molecular modeling showed that 4 a binds c‐myc G‐quadruplex DNA through an external end‐stacking mode at the 3′‐terminal face of the G‐quadruplex. Intriguingly, binding of c‐myc G‐quadruplex DNA by 3 b is accompanied by an increase of up to 38‐fold in photoluminescence intensity at λ_max=622 nm.     

Stabilization of G‐Quadruplex DNA with Platinum(II) Schiff Base Complexes: Luminescent Probe and Down‐Regulation of c‐myc Oncogene Expression

The interactions of a series of platinum(II) Schiff base complexes with c‐myc G‐quadruplex DNA were studied. Complex [PtL ^1a ] ( 1 a ; H₂L ^1a =N,N′‐bis(salicylidene)‐4,5‐methoxy‐1,2‐phenylenediamine) can moderately inhibit c‐myc gene promoter activity in a cell‐free system through stabilizing the G‐quadruplex structure and can inhibit c‐myc oncogene expression in cultured cells. The interaction between 1 a and G‐quadruplex DNA has been examined by ¹H NMR spectroscopy. By using computer‐aided structure‐based drug design for hit‐to‐lead optimization, an in silico G‐quadruplex DNA model has been constructed for docking‐based virtual screening to develop new platinum(II) Schiff base complexes with improved inhibitory activities. Complex [PtL ³ ] ( 3 ; H₂L ³ = N,N′‐bis{4‐[1‐(2‐propylpiperidine)oxy]salicylidene}‐4,5‐methoxy‐1,2‐phenylenediamine) has been identified with a top score in the virtual screening. This complex was subsequently prepared and experimentally tested in vitro for its ability to stabilize or induce the formation of the c‐myc G‐quadruplex. The inhibitory activity of 3 (IC₅₀=4.4 μM ) is tenfold more than that of 1 a . The interaction between 1 a or 3 with c‐myc G‐quadruplex DNA has been examined by absorption titration, emission titration, molecular modeling, and NMR titration experiments, thus revealing that both 1 a and 3 bind c‐myc G‐quadruplex DNA through an external end‐stacking mode at the 3’ terminal face of the G‐quadruplex. Such binding of G‐quadruplex DNA with 3 is accompanied by up to an eightfold increase in the intensity of photoluminescence at λ_max=652 nm. Complex 3 also effectively down‐regulated the expression of c‐myc in human hepatocarcinoma cells.     

Portrait of a Family of Highly Stabilizing and Selective Guanine Quadruplex Platinum(II)-Based Binders

The long-standing history of platinum coordination complexes in nucleic acid recognition attests to the unique suitability of such species for therapeutic applications. Here, we report the synthetic exploration and development of a family of di-imine ligands, and their platinum(II) complexes, elaborated on a 3-(2-pyridyl)-[1,2,4]triazolo[4,3-a]pyridine platform which, in its unsubstituted form, has recently been shown to display exceptional capabilities for guanine quadruplex (G4) targeting. The identification of facile, high-yielding synthetic methods for the derivatization of this platform for the incorporation of additional sites of interactions with guanine quadruplex loops and grooves, along with the optimization of platinum(II) complexation methods, are discussed. Gratifyingly, preliminary biophysical screening of this novel family of binders validates all but one family members as robust G4 binders and highlights enhanced selectivity for quadruplex versus duplex DNA compared to the parent compound. These results bear promise for practical developments based on this platform.     

Phosphorescent Platinum(II) Complexes with Mesoionic 1H‐1,2,3‐Triazolylidene Ligands

The synthesis and characterization of eight unprecedented phosphorescent C^C* cyclometalated mesoionic aryl‐1,2,3‐triazolylidene platinum(II) complexes with different β‐diketonate ligands are reported. All compounds proved to be strongly emissive at room temperature in poly(methyl methacrylate) films with an emitter concentration of 2 wt %. The observed photoluminescence properties were strongly dependent on the substitution on the aryl system and the β‐diketonate ligand. Compared to acetylacetonate, the β‐diketonates with aromatic substituents (mesityl and duryl) were found to significantly enhance the quantum yield while simultaneously reducing the emission lifetimes. Characterization was carried out by standard techniques, as well as solid‐state structure determination, which confirmed the binding mode of the carbene ligand. DFT calculations, carried out to predict the emission wavelength with maximum intensity, were in excellent agreement with the (later) obtained experimental data.     

A Conformationally Flexible Dinuclear PtII Complex with Differential Behavior of its Two States toward Quadruplex DNA

The reaction of tetrakis(pyridine‐2‐yl)pyrazine (tppz) with 2 equiv of (2,2′‐bpy)Pt^II in water yields two isomeric dinuclear cations, [{Pt(2,2′‐bpy)}₂(tppz)]⁴⁺, in which Pt coordination exclusively takes place through the two pairs of pyridine‐2‐yl nitrogen atoms. The two conformational isomers differ in their overall shape, with the formation of “Z” and “U” shapes, which are formed at 40 °C (Z isomer, 1 ) and under reflux conditions (U isomer, 2 ), respectively. X‐ray crystal‐structure analyses of the Z isomer, [{Pt(2,2′‐bpy)}₂(tppz)](PF₆)₄ ? 3 CHCl₃ ? 4 H₂O ( 1 a ), and of the U isomer, [{Pt(2,2′‐bpy)}₂](PF₆)₄ ? 2 CH₃CN ? 1.5 H₂O ( 2 a ), were carried out. Co‐crystallization of compound 2 with PtCl₂(2,2′‐bpy) yielded [{Pt(2,2′‐bpy)}₂(tppz)](BF₄)₄?[PtCl₂(2,2′‐bpy)] ? 4.5 H₂O ( 3 ), in which the PtCl₂(2,2′‐bpy) entity was sandwiched between the two 2,2′‐bpy faces of the U‐shaped cation ( 2 ). Quantum chemical calculations revealed that the U isomer was more stable than the Z isomer, both in the gas phase and in an aqueous environment. These two isomers display different affinities toward duplex DNA and human telomeric quadruplex DNA (Htelo), as concluded from CD spectroscopy and FID assays. Thus, the U isomer binds significantly more strongly to quadruplex DNA (DC₅₀=0.38 μM ) than the Z isomer (DC₅₀=8.50 μM ).     

Stereocontrol in Dinuclear Triple Lithium‐Bridged Titanium(IV) Complexes: Solving Some Stereochemical Mysteries

Compounds 1 a – f ‐H₂ form “monomeric” triscatecholate titanium(IV) complexes [Ti( 1 a – f )₃]^2?, which in the presence of Li cations are in equilibrium with the triple lithium‐bridged “dimers” [Li₃(Ti( 1 a – f )₃)₂]^?. The equilibrium strongly depends on the donor ability of the solvent. Usually, in solvents with high donor ability, the stereochemically labile monomer is preferred, whereas in nondonor solvents, the dimer is the major species. In the latter, the stereochemistry at the complex units is “locked”. The configuration at the titanium(IV) triscatecholates is influenced by addition of chiral ammonium countercations. In this case, the induced stereochemical information at the monomer is transferred to the dimer. Alternatively, the configuration at the metal complexes can be controlled by enantiomerically pure ester side chains. Due to the different orientation of the ester groups in the monomer or dimer, opposite configurations of the triscatecholates were observed by circular dichroism (CD) spectroscopy for [Ti( 1 c – e )₃]^2? or [Li₃(Ti( 1 c – e )₃)₂]^?. A surprising exception was found for the dimer [Li₃(Ti( 1 f )₃)₂]^?. Herein, the dimer is the dominating species in weak donor (methanol), as well as strong donor (DMSO), solvents. This is due to the bulkiness of the ester substituent destabilizing the monomer. Due to the size of the substituent in [Li₃(Ti( 1 f )₃)₂]^? the esters have to adopt an unusual conformation in the dimer resulting in a stereocontrol of the small methyl group. Following this, opposite stereocontrol mechanisms were observed for the central metal‐complex units of [Li₃(Ti( 1 c – e )₃)₂]^? or [Li₃(Ti( 1 f )₃)₂]^?.     

Synthesis and Luminescent Properties of an Acetylide-Bridged Dinuclear Platinum（Ⅱ） Terpyridyl Complex

An acetylide-bridged dinuclear platinum(Ⅱ) terpyridyl complex, [Pt(4‘-p-tolyl-terpy)-≡-phenyl-≡-(4‘-p-tolylterpy)Pt](ClO4)2 (1), has been successfully synthesized and its photophysical properties are reported.