Cationic corrole derivatives: a new family of G-quadruplex inducing and stabilizing ligands

Water-soluble cationic corrole derivatives were designed and synthesized, and the first observation of their interactions with the telomeric G-quadruplex was made.     

Cationic Pentaheteroaryls as Selective G‐Quadruplex Ligands by Solvent‐Free Microwave‐Assisted Synthesis

We report herein a solvent‐free and microwaved‐assisted synthesis of several water soluble acyclic pentaheteroaryls containing 1,2,4‐oxadiazole moieties ( 1 – 7 ). Their binding interactions with DNA quadruplex structures were thoroughly investigated by FRET melting, fluorescent intercalator displacement assay (G4‐FID) and CD spectroscopy. Among the G‐quadruplexes considered, attention was focused on telomeric repeats together with the proto‐oncogenic c‐kit sequences and the c‐myc oncogene promoter. Compound 1 , and to a lesser extent 2 and 5 , preferentially stabilise an antiparallel structure of the telomeric DNA motif, and exhibit an opposite binding behaviour to structurally related polyoxazole ( TOxaPy ), and do not bind duplex DNA. The efficiency and selectivity of the binding process was remarkably controlled by the structure of the solubilising moieties.     

Delineation of G‐Quadruplex Alkylation Sites Mediated by 3,6‐Bis(1‐methyl‐4‐vinylpyridinium iodide)carbazole‐Aniline Mustard Conjugates

A new G‐quadruplex (G‐4)‐directing alkylating agent BMVC‐C3M was designed and synthesized to integrate 3,6‐bis(1‐methyl‐4‐vinylpyridinium iodide)carbazole (BMVC) with aniline mustard. Various telomeric G‐4 structures (hybrid‐2 type and antiparallel) and an oncogene promoter, c‐MYC (parallel), were constructed to react with BMVC‐C3M, yielding 35 % alkylation yield toward G‐4 DNA over other DNA categories (<6 %) and high specificity under competition conditions. Analysis of the intact alkylation adducts by electrospray ionization mass spectroscopy (ESI‐MS) revealed the stepwise DNA alkylation mechanism of aniline mustard for the first time. Furthermore, the monoalkylation sites and intrastrand cross‐linking sites were determined and found to be dependent on G‐4 topology based on the results of footprinting analysis in combination with mass spectroscopic techniques and in silico modeling. The results indicated that BMVC‐C3M preferentially alkylated at A15 (H26), G12 (H24), and G2 (c‐MYC), respectively, as monoalkylated adducts and formed A15–C3M–A21 (H26), G12–C3M–G4 (H24), and G2–C3M–G4/G17 (c‐MYC), respectively, as cross‐linked dialkylated adducts. Collectively, the stability and site‐selective cross‐linking capacity of BMVC‐C3M provides a credible tool for the structural and functional characterization of G‐4 DNAs in biological systems.     

Molecular Recognition and Visual Detection of G‐Quadruplexes by a Dicarbocyanine Dye

The interactions of a dicarbocyanine dye 3,3′‐diethylthiadicarbocyanine, DiSC₂(5) , with DNA G‐quadruplexes were studied by means of a combination of various spectroscopic techniques. Aggregation of excess dye as a result of its positive charge is promoted by the presence of the polyanionic quadruplex structure. Specific high‐affinity binding to the parallel quadruplex of the MYC promoter sequence involves stacking of DiSC₂(5) on the external G‐tetrads; the 5′‐terminal tetrad is the favored binding site. Significant energy transfer between DNA and the dye in the UV spectral region is observed upon DiSC₂(5) binding. The transfer efficiency strongly depends on the DNA secondary structure as well as on the G‐quadruplex topology. These photophysical features enable the selective detection of DNA quadruplexes through sensitized DiSC₂(5) fluorescence in the visible region.     

Platinum phenanthroimidazole complexes as G-quadruplex DNA selective binders

Complexes that bind and stabilize G-quadruplex DNA structures are of significant interest due to their potential to inhibit telomerase and halt tumor cell proliferation. We here report the synthesis of the first Pt(II) G-quadruplex selective molecules, containing pi-extended phenanthroimidazole ligands. Binding studies of these complexes with duplex and quadruplex d(T(4)G(4)T(4))(4) DNA were performed. Intercalation to duplex DNA was established through UV/Vis titration, CD spectroscopy, and thermal denaturation studies. Significantly stronger binding affinity of these phenanthroimidazole Pt(II) complexes to G-quadruplex DNA was observed by UV/Vis spectroscopy and competitive equilibrium dialysis studies. Observed binding constants to quadruplex DNA were nearly two orders of magnitude greater than for duplex DNA. Circular dichroism studies show that an increase in pi-surface leads to a significant increase in the thermal stability of the Pt(II)/quadruplex DNA complex. The match in the pi-surface of these phenanthroimidazole Pt(II) complexes with quadruplex DNA was further substantiated by molecular modeling studies. Numerous favorable pi-stacking interactions with the large aromatic surface of the intermolecular G-quadruplex, and unforeseen hydrogen bonds between the ancillary ethylenediamine ligands and the quadruplex phosphate backbone are predicted. Thus, both biological and computational studies suggest that coupling the square-planar geometry of Pt(II) with pi-extended ligands results in a simple and modular method to create effective G-quadruplex selective binders, which can be readily optimized for use in telomerase-based antitumor therapy.     

Formation of Human Telomeric G-quadruplex Structures Induced by the Quaternary Benzophenanthridine Alkaloids:Sanguinarine,Nitidine,and Chelerythrine

The ligands which can facilitate the formation and stabilize G‐quadruplex structures have attracted enormous attention due to their potential ability of inhibiting the telomerase activity and halting tumor cell proliferation. It is noteworthy that the abilities of the quaternary benzophenanthridine alkaloids (QBAs), the very important G‐quadruplex binders, in inducing the formation of human telomeric DNA G‐quadruplex structures, have not been reported. Herein, the interaction between single‐strand human telomeric DNA and three QBAs: Sanguinarine (San), Nitidine (Nit) and Chelerythrine (Che), has been investigated. Although these molecules are very similar in structure, they exhibit significantly different abilities in inducing oligonucleotide d(TTAGGG)₄ (HT4) to specific G‐quadruplex structures. Our experimental results indicated that the best ligand San could convert HT4 into antiparallel G‐quadruplex structure completely, followed by Nit, which could transform to mixed‐type or hybrid G‐quadruplex structure partially, whereas Che could only transform to antiparallel G‐quadruplex structure in small quantities. The relative QBAs' inducing abilities as indicated by the CD data are in the order of San>Nit>Che. Further investigation revealed that the G‐quadruplex structures from HT4 induced by QBAs are of intramolecular motif. And only sequences with certain length could be induced by QBAs because of their positive charges which could not attract short chain DNA molecules to close to each other and form intermolecular G‐quadruplex. In addition, the factors that affect the interaction between HT4 and QBAs were discussed. It is proposed that the thickness of the molecular frame and the steric hindrance are the primary reasons why the subtle differences in QBAs' structure lead to their remarkable differences in inducing the formation of the G‐quadruplex structures.     

Bis(benzimidazole)pyridine derivative as a new class of G-quadruplex inducing and stabilizing ligand

Two new bis(benzimidazole)aryl derivatives have been prepared and one of them has been shown to induce and stabilize formation of a G-quadruplex.     

Alternative Synthesis and Structures of C‐monoacetylenic Phosphaalkenes

An alternative synthesis of C‐monoacetylenic phosphaalkenes trans‐Mes*P=C(Me)(C≡CR) (Mes* = 2, 4, 6‐^tBu₃Ph, R = Ph, SiMe₃) from C‐bromophosphaalkenes cis‐Mes*P=C(Me)Br using standard Sonogashira coupling conditions is described. Crystallographic studies confirm cis‐trans isomerization of the P=C double bond during Pd‐catalyzed cross coupling, leading exclusively to trans‐acetylenic phosphaalkenes. Crystallographic studies of all synthesized compounds reveal the extend of π‐conjugation over the acetylene and P=C π‐systems.     

Polycyclic Azoniahetarenes: Assessing the Binding Parameters of Complexes between Unsubstituted Ligands and G‐Quadruplex DNA

Polycyclic azoniahetarenes were employed to determine the effect of the structure of unsubstituted polyaromatic ligands on their quadruplex‐DNA binding properties. The interactions of three isomeric diazoniadibenzo[b,k]chrysenes ( 4 a – c ), diazoniapentaphene ( 5 ), diazoniaanthra[1,2‐a]anthracene ( 6 ), and tetraazoniapentapheno[6,7‐h]pentaphene ( 3 ) with quadruplex DNA were examined by DNA melting studies (FRET melting) and fluorimetric titrations. In general, penta‐ and hexacyclic azoniahetarenes bind to quadruplex DNA (K_b≈10⁶ M ^?1) even in the absence of additional functional side chains. The binding modes of 4 a – c and 3 were studied in more detail by ligand displacement experiments, isothermal titration calorimetry, and CD and NMR spectroscopy. All experimental data indicate that terminal π stacking of the diazoniachrysenes to the quadruplex is the major binding mode; however, because of different electron distributions of the π systems of each isomer, these ligands align differently in the binding site to achieve ideal binding interactions. It is proposed that tetraazonia ligand 3 binds to the quadruplex by terminal stacking with a small portion of its π system, whereas a significant part of the bulky ligand most likely points outside the quadruplex structure, and is thus partially placed in the grooves. Notably, 3 and the known tetracationic porphyrin TMPyP4 exhibit almost the same binding properties towards quadruplex DNA, with 3 being more selective for quadruplex than for duplex DNA. Overall, studies on azonia‐type hetarenes enable understanding of some parameters that govern the quadruplex‐binding properties of parent ligand systems. Since unsubstituted ligands were employed in this study, complementary and cooperative effects of additional substituents, which may interfere with the ligand properties, were eliminated.     

Helicates of chiragen-type ligands and their aptitude for chiral self-recognition

Two (-)-5,6-pinene-bipyridine moieties connected by a para-xylylene bridge (so-called chiragen-type ligands), (-)-L1, undergo self-assembly upon reaction with equimolar amounts of CuI to form enantiopure circular hexanuclear P-helicates. If both enantiomers of L1 are used, mixtures of P and M hexanuclear helicates are exclusively obtained through a complete chiral recognition; that is, no mixing of the (+) and (-) ligands, respectively, occurs upon complexation. This was proven by a) NMR spectroscopy where identical spectra to those for complexes with the enantiomerically pure ligands were obtained and b) circular dichroism (CD) spectroscopy. The reaction is completely changed by the use of the corresponding meso-L1. Instead of well-defined species, oligomeric mixtures are observed, a result demonstrating the crucial role played by ligand chirality in self-assembly processes. Structural variations on the chiral ligand L1, such as a meta-xylylene bridge instead of a para-xylylene one (in L4) or four pinene groups instead of two (in L5 and L6), favor nondiscrete coordination assembly.     

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.     

Tetraphenylethene Derivatives with Different Numbers of Positively Charged Side Arms have Different Multimeric G‐Quadruplex Recognition Specificity

Some G‐rich sequences in the human genome have the potential to fold into a multimeric G‐quadruplex (G4) structure and the formation of telomeric multimeric G4 has been demonstrated. Searching for highly specific multimeric G4 ligands is important for structure probing and for study of the function of G‐rich gene sequences, as well as for the design of novel anticancer drugs. We found different numbers of positively charged side‐arm substituents confer tetraphenylethene (TPE) derivatives with different multimeric G4 recognition specificity. 1,2‐Bis{4‐[(trimethylammonium)butoxy]phenyl}‐1,2‐tetraphenylethene dibromide (DATPE), which contains two side arms and gives a fluorescence response to only multimeric G4, has a low level of cytotoxicity and little or no effect on multimeric G4 conformation or stability. These features make DATPE a promising fluorescent probe for detection of multimeric G4 specifically in biological samples or in vivo. 1,1,2,2‐Tetrakis{4‐[(trimethylammonium)butoxy]phenyl}tetraphenylethene tetrabromide (QATPE), which contains four side arms, has a lower level of specificity for multimeric G4 recognition compared to DATPE but its binding affinity to multimeric G4 is higher compared to other structural DNAs. Its high multimeric G4‐binding affinity, excellent multimeric G4‐stabilizing ability, and the promotion of parallel G4 formation make QATPE a good candidate for novel anticancer drugs targeting multimeric G4 specifically, especially telomeric multimeric G4. This work provides information that might aid the design of specific multimeric G4 probes and the development of novel anticancer drugs.