opp-Dibenzoporphyrin Pyridinium Derivatives as Potential G-Quadruplex DNA Ligands.

Since the occurrence of tumours is closely associated with the telomerase function and oncogene expression, the structure of such enzymes and genes are being recognized as targets for new anticancer drugs. The efficacy of several ligands in telomerase inhibition and in the regulation of genes expression, by an effective stabilisation of G-quadruplexes (G4) DNA structures, is being considered as a promising strategy in cancer therapies. When evaluating the potential of a ligand for telomerase inhibition, the selectivity towards quadruplex versus duplex DNA is a fundamental attribute due to the large amount of double-stranded DNA in the cellular nucleus. This study reports the evaluated efficacy of three tetracationic opp-dibenzoporphyrins, a free base, and the corresponding zinc(II) and nickel(II) complexes, to stabilise G4 structures, namely the telomeric DNA sequence (AG3(T2AG3)3). In order to evaluate the selectivity of these ligands towards G4 structures, their interaction towards DNA calf thymus, as a double-strand DNA sequence, were also studied. The data obtained by using different spectroscopic techniques, such as ultraviolet-visible, fluorescence, and circular dichroism, suggested good affinity of the free-base porphyrin and of its zinc(II) complex for the considered DNA structures, both showing a pattern of selectivity for the telomeric G4 structure. A pattern of aggregation in aqueous solution was detected for both Zn(II) and Ni(II) metallo dibenzoporphyrins and the ability of DNA sequences to induce ligand disaggregation was observed.

Reaction of Corroles with Sarcosine and Paraformaldehyde: A New Facet of Corrole Chemistry.

Details on the unexpected formation of two new (dimethylamino)methyl corrole isomers from the reaction of 5,10,15-tris(pentafluorophenyl)corrolatogallium(III) with sarcosine and paraformaldehyde are presented. Semi-empirical calculations on possible mechanism pathways seem to indicate that the new compounds are probably formed through a Mannich-type reaction. The extension of the protocol to the free-base 5,10,15-tris(pentafluorophenyl)corrole afforded an unexpected new seven-membered ring corrole derivative, confirming the peculiar behavior of corroles towards known reactions when compared to the well-behaved porphyrin counterparts.

Interfacial assembly of zinc(II) phthalocyanines on graphene oxide (GO): Stable "turn-off-on" nanoplatforms to detect G-quadruplexes (G4).

HYPOTHESIS: The aggregation of phthalocyanines (Pcs) enfeebles their suitability as G-quadruplex (G4) ligands over time. It is hypothesized that the interfacial assembly of Pcs on graphene oxide (GO) influences intermolecular interactions, thereby affecting their physicochemical properties and inducing stabilization of Pcs in solution. Hence, the stacking of Pcs on GO could be tuned to create nanosystems with the ability to detect G4 for longer periods through a slow release of Pcs. EXPERIMENTS: Four cationic structurally-related zinc(II) phthalocyanines (ZnPc) were non-covalently assembled on GO by ultrasonic exfoliation. A comprehensive characterization of ZnPcs@GO was carried out by spectroscopic techniques and electron microscopy to understand the organization of ZnPcs on GO. The fluorescence of ZnPcs@GO was studied in the presence of G4 (T2G5T)4 and duplex ds26 through spectrofluorimetric titrations and monitored along time. FINDINGS: GO induced a re-organization of the ZnPcs mostly to J-aggregates and quenched their original fluorescence up to 98 % ("turn-off"). In general, ZnPcs@GO recovered their fluorescence ("turn-on") after the titrations and showed affinity to G4 (KD up to 1.92 µM). This is the first report that highlights the contribution of GO interfaces to assemble ZnPcs and allow their slow and controlled release to detect G4 over longer periods.

Diketopyrrolo[3,4-c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures.

Telomerase, oncogenes and tumor suppressors are closely associated with tumour occurrence, therefore these structures are being recognized as targets for the development of new anticancer drugs. The efficacy of several molecules in telomerase inhibition and regulation of genes expression, by adduct formation with G-quadruplexes (G4), has been studied by biophysical and biochemical methods with promising results. We report here the synthesis and structural characterization of a small positively charged diketopyrrolo[3,4-c]pyrrole derivative, identified as DPP(PyMe)2, that showed very promising results as G4 stabilizing ligand. The data obtained from UV-Vis and fluorescence experiments suggest that DPP(PyMe)2 presents high affinity to G4 structures. Docking studies and molecular dynamics simulations unraveled the binding modes of the ligand with four G4 structures. The obtained results also allowed us to conclude that the DPP(PyMe)2 ligand binds into the top G-tetrad or in a mixed binding mode depending on the GQ structure. A remarkable selectivity of DPP(PyMe)2 for c-MYC and KRAS 32R in the presence of ds26 was observed by circular dichroism (CD) and fluorescence resonance energy transfer (FRET) melting experiments. CD titrations revealed a stabilization higher than 30 °C in the case of c-MYC G4 structure and, for the same sequence, DPP(PyMe)2 showed the ability to block the activity of Taq polymerase in a dose-dependent manner. The subcellular localization obtained with confocal microscopy corroborates the results obtained by the other techniques and the obtained data suggest that DPP(PyMe)2 is an attractive ligand for the development of G4 labelling probes.

The Interactions of H2TMPyP, Analogues and Its Metal Complexes with DNA G-Quadruplexes-An Overview.

The evidence that telomerase is overexpressed in almost 90% of human cancers justifies the proposal of this enzyme as a potential target for anticancer drug design. The inhibition of telomerase by quadruplex stabilizing ligands is being considered a useful approach in anticancer drug design proposals. Several aromatic ligands, including porphyrins, were exploited for telomerase inhibition by adduct formation with G-Quadruplex (GQ). 5,10,15,20-Tetrakis(N-methyl-4-pyridinium)porphyrin (H2TMPyP) is one of the most studied porphyrins in this field, and although reported as presenting high affinity to GQ, its poor selectivity for GQ over duplex structures is recognized. To increase the desired selectivity, porphyrin modifications either at the peripheral positions or at the inner core through the coordination with different metals have been handled. Herein, studies involving the interactions of TMPyP and analogs with different DNA sequences able to form GQ and duplex structures using different experimental conditions and approaches are reviewed. Some considerations concerning the structural diversity and recognition modes of G-quadruplexes will be presented first to facilitate the comprehension of the studies reviewed. Additionally, considering the diversity of experimental conditions reported, we decided to complement this review with a screening where the behavior of H2TMPyP and of some of the reviewed metal complexes were evaluated under the same experimental conditions and using the same DNA sequences. In this comparison under unified conditions, we also evaluated, for the first time, the behavior of the AgII complex of H2TMPyP. In general, all derivatives showed good affinity for GQ DNA structures with binding constants in the range of 106-107 M-1 and ligand-GQ stoichiometric ratios of 3:1 and 4:1. A promising pattern of selectivity was also identified for the new AgII derivative.

Phthalocyanines for G-quadruplex aptamers binding.

The G-quadruplex (G4)-forming sequence within the AS1411 derivatives with alternative nucleobases and backbones can improve the chemical and biological properties of AS1411. Zn(II) phthalocyanine (ZnPc) derivatives have potential as high-affinity G4 ligands because they have similar size and shape to the G-quartets. The interactions of four Zn(II) phthalocyanines with the G4 AS1411 aptamer and its derivatives were determined by biophysical techniques, molecular docking and gel electrophoresis. Cell viability assay was carried out to evaluate the antiproliferative effects of Zn(II) phthalocyanines and complexes. CD experiments showed structural changes after addition of ZnPc 4, consistent with multiple binding modes and conformations shown by NMR and gel electrophoresis. CD melting confirmed that ZnPc 2 and ZnPc 4, both containing eight positive charges, are able to stabilize the AT11 G4 structure (ΔTm > 30 °C and 18.5 °C, respectively). Molecular docking studies of ZnPc 3 and ZnPc 4 suggested a preferential binding to the 3'- and 5'-end, respectively, of the AT11 G4. ZnPc 3 and its AT11 and AT11-L0 complexes revealed pronounced cytotoxic effect against cervical cancer cells and no cytotoxicity to normal human cells. Zn(II) phthalocyanines provide the basis for the development of effective therapeutic agents as G4 ligands.

Multicharged Phthalocyanines as Selective Ligands for G-Quadruplex DNA Structures.

The stabilization of G-Quadruplex DNA structures by ligands is a promising strategy for telomerase inhibition in cancer therapy since this enzyme is responsible for the unlimited proliferation of cancer cells. To assess the potential of a compound as a telomerase inhibitor, selectivity for quadruplex over duplex DNA is a fundamental attribute, as the drug must be able to recognize quadruplex DNA in the presence of a large amount of duplex DNA, in the cellular nucleus. By using different spectroscopic techniques, such as ultraviolet-visible, fluorescence and circular dichroism, this work evaluates the potential of a series of multicharged phthalocyanines, bearing four or eight positive charges, as G-Quadruplex stabilizing ligands. This work led us to conclude that the existence of a balance between the number and position of the positive charges in the phthalocyanine structure is a fundamental attribute for its selectivity for G-Quadruplex structures over duplex DNA structures. Two of the studied phthalocyanines, one with four peripheral positive charges (ZnPc1) and the other with less exposed eight positive charges (ZnPc4) showed high selectivity and affinity for G-Quadruplex over duplex DNA structures and were able to accumulate in the nucleus of UM-UC-3 bladder cancer cells.

Hybrids Based on Graphene Oxide and Porphyrin as Tools for Detection and Stabilization of DNA G-Quadruplexes.

Telomerase inhibition has been an important strategy in cancer therapies, but for which effective drugs are still required. Here, noncovalent hybrid nanoplatforms containing the tetracationic 5,10,15,20-tetrakis(1-methyl-pyridinium-4-yl)porphyrin (TMPyP) and graphene oxide (GO) were prepared for promoting telomerase inhibition through the selective detection and stabilization of DNA guanine-quadruplex (G-Q) structures. Upon binding TMPyP to the GO sheets, the typical absorption bands of porphyrin have been red-shifted and the fluorescence emission was quenched. Raman mapping was used for the first time to provide new insights into the role of the electrostatic and π-π stacking interactions in the formation of such hybrids. The selective recovery of fluorescence observed during the titration of TMPyP@GO with G-Q, resembles a selective "turn-off-on" fluorescence sensor for the detection of G-Q, paving the way for a new class of antitumor drugs.

Imidazole and imidazolium porphyrins: gas-phase chemistry of multicharged ions.

Electrospray ionization mass spectrometry/mass spectrometry in the positive ion mode was used to investigate the gas-phase chemistry of multicharged ions from solutions of porphyrins with 1,3-dimethylimidazolium-2-yl (DMIM) and 1-methylimidazol-2-yl (MIm) meso-substituents. The studied compounds include two free bases and 12 complexes with transition metals (Cu(II), Zn(II), Mn(III), and Fe(III)). The observed multicharged ions are either preformed or formed during the electrospraying process by reduction or protonation and comprise closed-shell and hypervalent mono-radical and bi-radical ions. The observed extensive and abundant fragmentation of the DMIM and MIm meso-substituents is a characteristic feature of these porphyrins. Fragments with the same mass values can be lost from the meso-substituents either as charged or neutral species and from closed-shell and hypervalent radical ions. Reduction processes are observed for both the free bases and the metallated DMIM porphyrins and occur predominantly by formation of hypervalent radicals that fragment, at low energy collisions, by loss of methyl radicals with formation of the corresponding MIm functionalities. These findings confirm that, when using electrospray ionization, reduction is an important characteristic of cationic meso-substituted tetrapyrrolic macrocycles, always occurring when delocalization of the formed hypervalent radicals is possible. For the Fe(III) and Mn(III) complexes, reduction of the metal centers is also observed as the predominant fragmentation of the corresponding reduced ions through losses of charged fragments testifies. The fragmentation of the closed-shell ions formed by protonation of the MIm porphyrins mirrors the fragmentation of the closed-shell ions of their DMIM counterparts.

Nonclassic metallointercalators with dipyridophenazine: DNA interaction studies and leishmanicidal activity.

Complexes [Cu(CH3COO)(dppz)2]CH3COO (1) and [Zn(dppz)2](BF4)2 (2) with the intercalator dipyridophenazine (dppz) were prepared to obtain metallointercalators with increased geometrical flexibility compared to octahedral ones. Biophysical results (thermal denaturation, circular dichroism, rheometry, atomic force microscopy) indicate a strong interaction with DNA by intercalation and the existence of a positive cooperative effect with groove binding being preferred at low concentration of complexes. Induced circular dichroism (ICD) studies with DNA show that compounds 1 and 2 have a preferred orientation when binding to DNA. Since the compounds lack functional groups to permit hydrogen bonds, a combined intercalation/covalent binding mode is plausible. Further studies by QTof-ESI-MS and tandem experiments with GC oligonucleotides strongly support this dual-binding mode, since binding requires loss of one dppz unit with the copper center remaining attached to DNA even after another dppz loss. DNA saturation by the copper compound occurs at about one-half the concentration required for the zinc complex. Molecular modeling results suggest that it is caused by the increased ability of Cu(II) to distort to a more planar structure during interaction with DNA. Compounds 1 and 2 are active against a viscerotropic Leishmania infantum strain at submicromolar concentrations (IC50 = 0.57 and 0.46 µM, respectively), being more active than the reference drug miltefosine (M) (15.97 µM). They are also more cytotoxic than the control on human macrophages (MTD25 = 0.41 (1), 0.63 (2)). Besides miltefosine, the zinc compound is the only one with a MTD25/IC50 ratio above 1 on the promastigote phase (1.39) and was further studied on the amastigote form with a significant improvement in the therapeutic index (2.51). Combined analysis of DNA biophysical studies, parasite activity, and cytotoxicity measurements suggests that intercalation correlates with leishmanicidal activity, while cytotoxicity results are justified by a combination of DNA intercalation and possible radical formation in the case of Cu(II), most probably hydroxyl and/or singlet oxygen radicals.

Differentiation of aminomethyl corrole isomers by mass spectrometry.

Two new isomeric aminomethyl corrole derivatives of [5,10,15-tris(pentafluorophenyl)corrolato]gallium(III) were synthesized with pyridine (py) molecules as axial ligands. When investigated by electrospray ionization mass spectrometry, in the positive and the negative ion modes, these compounds showed an unusual gas-phase behavior that could be used for their differentiation. In the positive ion mode, the differentiation was achieved through the formation of diagnostic fragment ions formed from [M-py + H](+) precursors, by (CH(3) )(2) NH and HF losses. An unusual addition of water to the main fragment ions provides an alternative route for isomer identification. Semi-empirical calculations were performed to elucidate the structures and stabilities of the main ionic species formed in the positive ion mode. In the negative ion mode isomer discrimination is accomplished via the fragmentation of the methoxide adduct ions [M-py + CH(3) O](-) through (CH(3) )(2) N(.) and HF losses.

Charge and substituent effects on the stability of porphyrin/G-quadruplex adducts.

The adduct ions of two tetramolecular G-quadruplexes formed from the d(TGGGGT) and d(TTGGGGGT) single strands with a group of cationic porphyrins, with different charges and substituents, and one neutral porphyrin, were investigated by ESI-MS and ESI-MS/MS in the negative ion mode. Formation of [Q + nNH(4)(+)+P(p+)-(z + n + p)H(+)](z-) adduct ions (where Q = quadruplex, n = number of quartets minus 1, P = porphyrin and p(+) = 0,1,2,3,4) indicates that the porphyrins are bound outside the quadruplexes providing an additional stabilization to those structures. The fragmentation pathways of the [Q + nNH(4)(+)+P(p+)-(z + n + p)H(+)](z-) adduct ions depend on the number of positive charges (p(+)) of the porphyrins and on the overall complex charge (z(-)), but do not show a significant dependence on the type of the substituent groups in the porphyrins. Formation of the 'unfilled' ions [Q + P(p+)-(z + p)H(+)](z-) predominates for porphyrins with a higher number of positive charges. Strand separation with the formation of [T + P(p+)-(z-2 + p)H(+)]((z-2)-) and (SS-2H(+))(2-) ions, where T = [d(TG(4)T)](3) and [d(T(2)G(5)T)](3) and SS = d(TG(4)T) and d(T(2)G(5)T) is only observed for the complexes with a higher overall negative charge. Porphyrin loss with the formation of [Q + nNH(4)(+)-(z + n)H(+)](z-) ions occurs predominantly for the neutral and monocharged porphyrins. The predominant formation of the 'unfilled' ions, [Q + P(p+)-(z + n)H(+)](z-), for porphyrins with a higher number of charges shows that these porphyrins can prevent strand separation and preserve, at least partially, the quadruplex structure.

Gas-phase fragmentation of protonated C60-pyrimidine derivatives.

Electrospray ionization mass spectrometry/mass spectrometry (ESI/MS/MS) and multiple stage mass spectrometry (MSn, n > 2) were used in the positive ion mode, with two different types of mass spectrometers, a quadrupole time-of-flight and an ion trap, to characterize two sets of different types of C60-aminopyrimidine exohedral derivatives. In one set, the pyrimidine moiety bears an amino acid methyl ester residue, and in the other the pyrimidine ring is part of a nucleoside-type moiety, the latter existing as two separated diastereoisomers.We have found that retro-cycloaddition processes occur for the closed shell protonated species formed by electrospraying C60 derivatives synthesized by Diels-Alder reactions, whereas for the C60 derivatives synthesized via 1,3-dipolar cycloadditions, these processes did not occur. Formation of diagnostic ions allowed the differentiation between the two groups of fullerene derivatives, and between the diastereoisomers of C60 derivatives with a nucleoside-type moiety. In general, the fragmentation processes are strongly dependent on the protonation sites and on the structure of the exohedral moieties.

Reduction and adduct formation from electrosprayed solutions of porphyrin salts.

The solutions of four meso-tetrakis(N-alkylpyridinium-4-yl)porphyrin salts and of the p-toluenesulfonate salt of meso-tetrakis(4-trimethylammoniumphenyl)porphyrin, in methanol, were studied by electrospray mass spectrometry, in order to investigate the influence of the type of counter ion, the length of the substituent N-alkyl groups of the four (N-alkylpyridinium-4-yl)porphyrins and the presence of an aromatic (alkylpyridinium) or aliphatic (trimethylammonium) nitrogen, in ion formation. In our experimental conditions, adducts with the counter ions were formed only for the meso-tetrakis(4-trimethylammoniumphenyl)porphyrin and were not observed for the other porphyrins, even when the counter ion was the same. In contrast, formation of reduced species, such as the [M(4+) + e(-)]3+, [M(4+) + 2e(-)]2+, [M(4+) + 4e(-) + 2H(+)]2+, and [M(4+) + 5e(-) + 2H(+)]+ ions was observed only for the (N-alkylpyridinium-4-yl)porphyrins and the appearance of these species is apparently solvent related and may occur via counter ion/solvent adducts.

Reduction of cationic free-base meso-tris-N-methylpyridinium-4-yl porphyrins in positive mode electrospray ionization mass spectrometry.

Reductions involving more than one electron with formation of the M+ and [M+2H]+ ions were observed for electrosprayed meso-tris(N-methylpyridinium-4-yl)porphyrin iodides, MI3. These reductions were studied by using different solvents and flow rates. Formation of the [M+2H]+ ions occurred only for protic solvents and to a larger extent at lower flow rates. The type of the fourth substituent does not seem to affect the reduction processes. Formation of the two reduced species, M+ and [M+2H]+ ions, may occur through the participation of counter ion/solvent clusters. Reduction of multiply charged, non-metallated species with formation of [M+nH]+ ions (n > 1) was not observed before in positive mode electrospray mass spectrometry.

Interactions of cationic porphyrins with double-stranded oligodeoxynucleotides: a study by electrospray ionisation mass spectrometry.

Electrospray ionisation mass spectrometry (ESI-MS), electrospray ionisation tandem mass spectrometry (ESI-MS/MS) and Ultraviolet-visible (UV-vis) spectroscopy were used to investigate the non-covalent interactions between small oligonucleotide duplexes with the GC motif and a group of cationic meso(N-methylpyridynium-4-yl)porphyrins (four free bases with one to four positive charges, and the zinc complex of the tetracationic free base). The results obtained point to outside binding of the porphyrins, with the binding strength increasing with the number of positive charges. Fragmentations involving losses from both chains were observed for the porphyrins with N-methylpyridinium-4-yl groups in opposite meso positions.