DNA binding and photocleavage properties of a novel cationic porphyrin-anthraquinone hybrid

Hook, Line, and Sinker! Spectroscopic Studies of Bi-Modular Mono- and Bis-1,8-naphthalimide-Ru(bpy)3-conjugates as DNA "Light Switches"

Bi-chromophoric ruthenium polypyridyl complexes comprising one or two nitro-1,8-naphthalimide groups are shown to be effective DNA binders with off-on light switching properties. The binding to DNA was investigated using a combination of studies such as UV-visible absorption and emission titrations, thermal denaturation, and circular dichroism spectroscopy. The DNA affinity was shown to be sensitive to both the linker length and the number of naphthalimides (one vs two) contained in these systems and binding constants ranging from 10⁶ to 10⁷ M^-1 for salmon testes DNA. The strong DNA binding is attributed to the combination of naphthalimide intercalation and the electrostatic interaction of the ruthenium complex. Large emission enhancements from the metal to ligand charge transfer (MLCT) emission arising from the metal complex were observed upon DNA binding, which was attributed to the interruption of intramolecular electron transfer quenching processes. Moving the nitro substitution from the 4-position to the 3-position is found to result in modification of the DNA binding and the resulting optical properties. The off-on light switch phenomena reported demonstrate the potential of these complexes to act as DNA probes.

Carbazole appended trans-dicationic pyridinium porphyrin finds supremacy in DNA binding/photocleavage over a non-carbazolyl analogue

A carbazolyl appended trans-pyridyl porphyrin (1) was synthesized and its dicationic form 2 was obtained by methylation of the pyridyl group. Copper and zinc complexes of porphyrin 2 (Cu(II), 3; Zn(II), 4) were isolated and characterized by various modern spectroscopic techniques. The DNA binding properties of 2, 3, and 4 have been explored against calf thymus-DNA (CT-DNA). DNA binding was quantized using the intrinsic binding constant (K_b) that was calculated by UV-visible absorption spectroscopy, and the value K_b = 1.6 × 10⁶ M^-1 for compound 2 reveals a better interaction of 2 towards CT-DNA than those of 3 (3.1 × 10⁵ M^-1) and 4 (3.4 × 10⁵ M^-1), which follows the order 2 > 4 > 3. The fluorescence quenching efficiency and ethidium bromide quenching assay also indicated a good binding affinity of all the compounds towards CT-DNA. Furthermore, the spectroscopic data suggest that the possible mode of interaction is intercalation. The docking studies were in accordance with the experimental results. Notably, DNA cleavage studies reveal that 2 shows better damage than 3 and 4 which is in accordance with the binding affinity order 2 > 4 > 3. The observed quantum yield (2: 0.65, 3: 0.33, and 4: 0.97) and no change in DNA cleavage in the presence of NaN₃ reveal the involvement of singlet oxygen. The singlet excited state lifetimes were in the range of 6.3-1.2 ns. Furthermore, these porphyrins can be investigated as interesting photosensitizers in photodynamic therapy and photochemotherapy.

Interactions of porphyrins with DNA: A review focusing recent advances in chemical modifications on porphyrins as artificial nucleases

The advance of porphyrins as artificial nucleases along the years have developed a class of compounds having potential therapeutic applications. Being an extrovert of chemistry, a variety of chemical modifications have been done on porphyrin macrocycle in order to improve the spectroscopic properties and to adapt as artificial receptors that can recognize molecules. The last twenty years has witnessed broad research in the arena of porphyrin- DNA interactions and their evolution from simple to more complex entities. In this review, we summarize the recent advances in the porphyrin-based structural modifications, with a specific emphasis on various effects of porphyrin on DNA cleavage potency. We particularly detailed the nuclease activity of cationic and anionic porphyrins, porphyrin dimers and conjugates as well as heme proteins till the third generation porphyrins as artificial nucleases.

Synthesis, electrochemistry, DNA binding and in vitro cytotoxic activity of tripodal ferrocenyl bis-naphthalimide derivatives

A series of tripodal ferrocenyl bis-naphthalimide derivatives were synthesized and characterized. All of the bis-naphthalimide derivatives exhibited good DNA binding ability which was confirmed by ethidium bromide (EB) displacement experiment and ultraviolet (UV)-visible absorption titration. And the binding mode of these compounds was proved to be a hybrid binding mode by experiments. The cytotoxicity of synthesized compounds against 4 different human cancer cell lines (EC109, BGC823, SGC7901 and HEPG2) was evaluated by thiazolyl blue tetrazolium bromide (MTT) assay. All of the bis-naphthalimide derivatives exhibited good anticancer activity than the positive control drug (amonafide), which was due to the promotion of reactive oxygen species (ROS) level in test cancer cells by the reversible one-electron redox process of ferrocenyl bis-naphthalimide derivatives. Although there was no obvious relationship between the binding constants and the chain length, the structure cytotoxicity relationship revealed that the linker of n = 3, m = 1 was the best choice for the tested tripodol bis-naphthalimide derivatives. SYNOPSIS: A series of tripodal ferrocenyl bis-naphthalimide derivatives were synthesized to study the DNA binding ability and the cytotoxicity induced by reactive oxygen species. All of the compounds exhibited good DNA binding ability. And the structure cytotoxicity relationship revealed that the structure of 5h was the best choice.

A promising anticancer drug: a photosensitizer based on the porphyrin skeleton

Photodynamic therapy (PDT) is a minimally invasive combination of treatments that treat tumors and other diseases by using photosensitizers, light and oxygen to produce cytotoxic reactive oxygen species (ROS) inducing tumor cell apoptosis. Photosensitizers are the key part of PDT for clinical application and experimental research, and most of them are porphyrin compounds at present. Due to their unique affinity for tumor tissues, porphyrins are not only excellent photosensitizers, but also good carriers to transport other active drugs into tumor tissues, which can exert synergistic anticancer effects of PDT and chemotherapy. This article reviews the clinical development of porphyrin photosensitizers and the research status of porphyrin containing bioactive groups. Finally, future perspectives and the current challenges of photosensitizers based on the porphyrin skeleton are discussed.

Sequence selective photoinduced electron transfer of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to various DNAs (calf thymus DNA (Ct-DNA), poly[d(G-C)2], and poly[d(A-T)2]) have been investigated using circular dichroism and linear dichroism measurements. Based on the polarization spectroscopic results, it can be shown that the pyrenyl and porphryin planes are skewed to a large extent for PyTMPyP in an aqueous environment and in the binding site of poly[d(G-C)2]. In this complex, a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties occurs. On the other hand, PET was not observed in the PyTMPyP-poly[d(A-T)2] complex, whereas the fluorescence intensity of TMPyP was enhanced. The molecular planes of the pyrene and porphyrin moieties are almost parallel in the poly[d(A-T)2] and Ct-DNA adducts. Moreover, the generation of 1O2 species occurs only for the PyTMPyP-Ct-DNA and PyTMPyP-poly[d(A-T)2] complexes. We discuss the photophysical properties of PyTMPyP which are attributed to the binding patterns and the sequence of DNA bases.

Study on antitumor molecular mechanism of Alisols based on p53DNA

Methyl thiazolyl tetrazolium (MTT) assay, UV-vis absorption spectroscopy, fluorescence spectroscopy and molecular simulation were used to investigate the antitumor activity of alisol A, alisol B and an 1:1 mixture of both compounds, the mechanism of its interaction with anti-cancer target p53DNA and explored the antitumor mechanism of alisols. MTT assay showed that the order of antitumor activity was:alisol B > alisol A > alisol A-alisol B(1:1). Spectroscopic experiments and molecular simulation suggested that alisol A, alisol B and their mixture interact with p53DNA in by partial insertion and the strength of binding affinity was consistent with the MTT assay. The K_sv of alisol A was 9.35 × 10⁴ L·mol^-1, K_q was 9.35 × 10¹² L·mol^-1·s^-1 and the K_sv and K_q of alisol B were 11.61 × 10⁴ L·mol^-1 and 11.61 × 10¹² L·mol^-1·s^-1. The molecular simulation revealed that competitive antagonism was observed in the interaction between the alisol mixture and p53DNA. The critical groups and significant binding sites for the interaction between alisol monomers and p53DNA include C19-OH and C22-OH of the alisols; N2 and H21 of the guanine deoxynucleotide (DG8), N2-H21 of the DG7, O4' of the DG9 in the f-chain of p53DNA; and C2-O2 of the cytosine deoxynucleotide (DC16) in the e-chain of p53DNA. Also, the C-22 and C23- of the alisols and the DA18-DT5 base pairs of p53DNA were key factors in the interaction of the mixture with p53DNA.

Synthetic methodologies leading to porphyrin-quinone conjugates

This review focuses on synthetic strategies that have been established for the preparation of porphyrin-quinone conjugates of potential biological significance and as donor–acceptor compounds for electron transfer processes.

Binding of Metallated Porphyrin-Imidazophenazine Conjugate to Tetramolecular Quadruplex Formed by Poly(G): a Spectroscopic Investigation

The binding of telomerase inhibitor ZnTMPyP(3+)-ImPzn, Zn(II) derivative of tricationic porphyrin-imidazophenazine conjugate, to tetramolecular quadruplex structure formed by poly(G) was studied in aqueous solutions at neutral pH and near physiological ionic strength using absorption and polarized fluorescent spectroscopy techniques. Three binding modes were determined from the dependences of the fluorescence intensity and polarization degree for the porphyrin and phenazine moieties of the conjugate on molar polymer-to-dye ratio (P/D). The first one is outside electrostatic binding of positively charged porphyrin fragments to anionic phosphate groups of the polymer which prevails only at very low P/D values and manifests itself by substantial fluorescence quenching. It is suggested that the formation of externally bound porphyrin dimers occurs. The other two binding modes observed at high P/D are embedding of the ZnTMPyP(3+) moiety into the groove of poly(G) quadruplex accompanied by more than 3-fold enhancement of the conjugate emission, and simultaneous intercalation of the phenazine fragment between the guanine bases accompanied by the increase of its fluorescence polarization degree up to 0.25. Thus Zn(II) conjugate seems to be promising ligand for the stabilization of G-quadruplex structures since porphyrin binding to poly(G) is strengthened by additional intercalation of phenazine moiety.

Spectroscopic Studies on Binding of Porphyrin-Phenazine Conjugate to Four-Stranded Poly(G)

Binding of a novel cationic porphyrin-imidazophenazine conjugate, TMPyP(3+)-ImPzn, to four-stranded poly(G) was investigated in aqueous solutions of neutral pH under near physiological ionic conditions using absorption, polarized fluorescent spectroscopy and fluorescence titration techniques. In absence of the polymer the conjugate folds into stable internal heterodimer with stacking between the porphyrin and phenazine chromophores. Binding of TMPyP(3+)-ImPzn to poly(G) is realized by two competing ways. At low polymer-to-dye ratio (P/D < 6) outside electrostatic binding of the cationic porphyrin moieties of the conjugate to anionic polynucleotide backbone with their self-stacking is predominant. It is accompanied by heterodimer dissociation and distancing of phenazine moieties from the polymer. This binding mode is characterized by strong quenching of the conjugate fluorescence. Increase of P/D results in the disintegration of the porphyrin stacks and redistribution of the bound conjugate molecules along the polymer chain. At P/D > 10 another binding mode becomes dominant, embedding of TMPyP(3+)-ImPzn heterodimers into poly(G) groove as a whole is occurred.

Synthesis, DNA-binding, and photocleavage properties of a serious of porphyrin-daunomycin hybrids

It is widely accepted that the pharmacological activities of anthracyclines antitumor agents express when the quinone-containing chromophore intercalates into base pairs of the duplex DNA. We have successfully synthesized and investigated the DNA-interactions of hybrids composed with quinone chromophore and cationic porphyrin. Herein, a clinic anticancer drug, daunomycin, is introduced to the porphyrin hybrids through different lengths of amide alkyl linkages, and their interactions and cleavage to DNA were studied compared with the previous porphyrin-quinone hybrids. Spectral results and the determined binding affinity constants (Kb) show that the attachment of daunomycin to porphyrin could improve the DNA-binding and photocleaving abilities. The porphyrin-daunomycin hybrids may find useful employment in investigating the ligand-DNA interaction.

The binding modes of cationic porphyrin-anthraquinone hybrids to DNA duplexes: in silico study

Cationic porphyrin-anthraquinone hybrids bearing peripheral substituents, either pyridine, imidazole, or pyrazole rings have been investigated for their binding mode to DNA duplexes. The four kinds of DNA duplexes were used, which represent intercalation and groove binding modes. AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, while monitoring of conformational changes of four best hybrid-DNA complexes during 2 ns was performed by Amber9 molecular dynamics package. The binding energy calculation of best four complexes was then carried out using MMPBSA method. The hybrid compounds interacted to DNA duplexes through intercalation and groove binding modes. The minor groove binding of DNA was energetically preferred by cationic porphyrin hybrids due to favorable electrostatic and van der Waals interactions. Both electrostatic and van der Waals contributions were able to distinguish the binding mode of porphyrin hybrid to DNA duplexes.

Magneto-structural correlation, antioxidant, DNA interaction and growth inhibition activities of new chloro-bridged phenolate complexes

The consistent stability constants as well as antioxidant, DNA interaction and cytotoxicity efficacy of chloro-bridged complexes have been established.

DNA oligonucleotide templated nanohybrids using electronic type sorted carbon nanotubes for light harvesting

Light harvesting nanostructure hybrids have been designed and demonstrated using single-wall carbon nanotubes (SWCNTs) and porphyrin chromophores. DNA oligonucleotides are used to conjugate SWCNTs with light-absorbing chromophores for transparent films which generate photocurrents. High-purity semiconducting SWCNTs demonstrate significant enhancement in the photocurrent compared to metallic or unsorted tubes.

Synthesis, RNA binding and nuclease activity of porphyrin-hydroxamic acid derivatives

The interaction modes and nuclease activity against RNA of methylpyridiniumyl/phenyl-hydroxamic acid porphyrin adducts have been investigated. These compounds are derived from the tetracationic meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin (H2TMPyP-4) by replacing one or two pyridinium rings with a phenyl group. This group is bearing an aliphatic chain of three carbon atoms in the para position to a hydroxamic acid. A different interaction mode is observed depending on the number of charges and hydroxamic acid function. The nuclease activity of the porphyrin adducts against RNA has been demonstrated. Also the effect of the presence of various lanthanide ions on the porphyrin nuclease activity has been tested.

Cationic pyridinium porphyrins appending different peripheral substituents: spectroscopic studies on their interactions with bovine serum albumin

The interaction of cationic pyridinium porphyrins appending methylpyridyl, hydroxyphenyl, propionoxyphenyl or carboxyphenyl group at meso-20-position of porphyrin core with bovine serum albumin (BSA), was studied by the combination of absorption spectroscopy, surface-enhanced Raman spectroscopy (SERS), circular dichroism (CD) spectroscopy, fluorescence spectroscopy and synchronous spectroscopy. The spectral monitoring results indicate that the studied compounds could bind with the BSA molecule and the calculated binding constants show that the tetracationic porphyrin has higher binding affinity than those tricationic ones. The interactions between porphyrins and BSA employ an electrostatic binding mechanism and there was only one binding site which located on the surface of the protein molecule.

Synthesis, DNA binding, and cleavage studies of novel PNA binding cyclen complexes

A novel coumarin-appended PNA binding cyclen derivative ligand, C1, and its copper(II) complex, C2, have been synthesized and characterized. The interaction of these compounds with DNA was systematically investigated by absorption, fluorescence, and viscometric titration, and DNA-melting and gel-electrophoresis experiments. DNA Melting and viscometric titration experiments indicate that the binding mode of C1 is a groove binding, and C2 is a multiple binding mode that involves groove binding and electrostatic binding. From the absorption-titration data, we can state that the primary interaction between CT DNA and the two compounds may be H-bonds between nucleobases. Fluorescence studies indicate that the binding ability of C1 to d(A)(9) is as twice or thrice as that of other oligodeoxynucleotides. Agarose gel-electrophoresis experiments demonstrate that C2 is an excellent chemical nuclease, which can cleave plasmid DNA completely within 24 h.

DNA binding and photocleavage specificities of a group of tricationic metalloporphyrins

The interactions of 5,10,15-tris(1-methylpyridinium-4-yl)-20-(4-hydroxyphenyl)porphyrinatozinc(II) Zn[TMPyHP](3+) (2) along with Cu[TMPyHP](3+) (3), Co[TMPyHP](4+) (4), Mn[TMPyHP](4+) (5) and the free base porphyrin H(2)[TMPyHP](3+) (1) with duplex DNA have been studied by using a combination of absorption, fluorescence titration, surface-enhanced Raman spectroscopy (SERS), induced circular dichroism (ICD) spectroscopy, thermal DNA denaturation, viscosity measurements as well as gel electrophoresis experiment. Their binding modes and intrinsic binding constants (K(b)) to calf DNA (CT DNA) were comparatively studied and were found significantly influenced by different metals coordinated with the porphyrin plane. Except 3, which has four-coordination structure at the metal, all the metal derivatives showed non-intercalative DNA-binding mode and lower K(b) than the free base porphyrin 1, most probably due to the steric hindrance results from the axial ligands of the inserted metals which are five or six-coordination structures. Meanwhile, the insertion of metals into cationic porphyrin greatly removed the self-aggregation of the metal-free porphyrins, and thus fully enhanced the singlet oxygen ((1)O(2)) productivities in the DNA photocleavage experiments. Therefore, these metalloporphyrins have comparable DNA cleavage ability with the free base porphyrin.