Study on the interaction of new water-soluble porphyrin with DNA

Light exposure of tetra-cationic porphyrins containing peripheral Pd(II)-bipyridyl complexes and the induced effects on purified DNA molecule, fibroblast and melanoma cell lines

Photodynamic therapy (PDT) combines a light source, oxygen, and a photosensitizer (PS) to generate reactive oxygen species (ROS) for treating diseases. In this study, we evaluated two meso-tetra-pyridyl porphyrins with [Pd(bpy)Cl]+, namely 3-PdTPyP and 4-PdTPyP, as PS for PDT application. DNA interaction was assessed by spectroscopic measurements (UV-Vis and fluorescence emission), viscosity analysis, and molecular docking simulations. The results indicate that Pd(II)-porphyrins do not intercalate into DNA, suggesting that the minor groove is the primary interaction site, mainly through van der Waals forces. These metalloporphyrins effectively induced nitrogenous bases oxidation, particularly in purines, after white light irradiation. The induced DNA lesions were able to inactivate plasmid DNA metabolism (DNA replication and transcription) in a bacterial model. 3-PdTPyP and 4-PdTPyP significantly decreased the viability of treated melanoma cell lines (A375 and B16-F10), demonstrating that melanoma cell lines were more sensitive to these Pd(II)-porphyrins than the fibroblast cell line (L929). Moreover, 3-PdTPyP was more photototoxic to A375 cells (IC50 = 0.43 μM), whereas 4-PdTPyP was more photototoxic to B16-F10 cells (IC50 = 0.51 μM). These findings suggest that these porphyrins are promising PS for future PDT research focused on skin cancer.

Plasmonic Surface of Metallic Gold and Silver Nanoparticles Induced Fluorescence Quenching of Meso-Terakis (4-Sulfonatophenyl) Porphyrin (TPPS) and Theoretical-Experimental Comparable

Colloidal metallic nanoparticles have attracted a lot of interest in the last two decades owing to their simple synthesis and fascinating optical properties. In this manuscript, a study of the effect of both gold nanoparticles (Au NPs) and silver nanoparticles (Ag NPs) on the fluorescence emission (FE) of TPPS has been investigated utilizing steady-state fluorescence spectroscopy and UV–Vis spectrophotometry. From the observed electronic absorption spectra, there is no evidence of the ground state interaction between metallic Au NPs or Ag NPs with TPPS. On the other side, the FE spectra of TPPS have been quenched by both Ag and Au NPs. Via applying quenching calculations, Ag NPs showed only traditional static fluorescence quenching of TPPS with linear Stern–Volmer (SV) plots. On the contrary, quenching of TPPS emission by Au NPs shows composed models. One model is the sphere of action static quenching model that prevails at high quencher concentrations leading to non-linear SV plots with positive deviation. However, at low Au NPs concentrations, traditional dynamic quenching occurs with linear SV plots. The quantum calculations for TPPS structure have been obtained using Gaussian 09 software: in which the TPPS optimized molecular structure was achieved using DFT/B3LYP/6-311G (d) in a gaseous state. Also, the calculated electronic absorption spectra for the same molecule in water as a solvent are obtained using TD/M06/6-311G +  + (2d, 2p). Furthermore, the theoretical and experimental results comparable to UV–Vis spectra have been investigated.

DNA-binding, photocleavage and anti-cancer activity of tin(IV) corrole

A new tin(IV) corrole, 5,10,15-tris(4-methoxycarbonylphenyl) corrole tin(IV) (1-Sn) was synthesized and characterized. The DNA binding, photocleavage and anti-cancer activity were studied and compared with its free-base. The interaction of 1-Sn and its free-base 1 with calf thymus DNA had been investigated by spectroscopic methods, viscosity measurements and molecular docking analysis. The results revealed that 1-Sn and 1 could interact with calf thymus DNA via an outside groove binding mode. Furthermore, although 1 displayed no photonuclease activity, 1-Sn exhibited good photonuclease activity as indicated by agarose gel electrophoresis, and superoxide anion might be the active intermediate for the DNA scission. Finally, 1 was nontoxic but 1-Sn displayed cytotoxicity towards A549 tumor cell lines.

Water-soluble Manganese and Iron Mesotetrakis(carboxyl)porphyrin: DNA Binding, Oxidative Cleavage, and Cytotoxic Activities

Two new water-soluble metal carboxyl porphyrins, manganese (III) meso-tetrakis (carboxyl) porphyrin and iron (III) meso-tetrakis (carboxyl) porphyrin, were synthesized and characterized. Their interactions with ct-DNA were investigated by UV-Vis titration, fluorescence spectra, viscosity measurement and CD spectra. The results showed they can strongly bind to ct-DNA via outside binding mode. Electrophoresis experiments revealed that both complexes can cleave pBR322 DNA efficiently in the presence of hydrogen peroxide, albeit 2-Mn exhibited a little higher efficiency. The inhibitor tests suggest the oxidative DNA cleavage by these two complexes may involve hydroxyl radical active intermediates. Notably, 2-Mn exhibited considerable photocytotoxicity against Hep G2 cell via triggering a significant generation of ROS and causing disruption of MMP after irradiation.

The magnetic properties, DNA/HSA binding and nuclease activity of manganese N-confused porphyrin

The first oxidative cleavage of DNA by manganese [Formula: see text]-confused porphyrin [chloro(2-aza-2-methyl-5,10,15,20-tetrakis([Formula: see text]-chlorophenyl)-21-carbaporphyrin)manganese(III), 1] using H2O2 as oxidant agent and its magnetic, calf thymus DNA(ct-DNA)- and human serum albumin (HSA) binding properties were investigated. The magnitude of the axial (D) zero-field splitting for the mononuclear Mn(III) center in 1 was determined to be approximately 2.71 cm[Formula: see text] by paramagnetic susceptibility measurements. The DNA- and HSA binding experimental results showed that 1 bound to ct-DNA via an outside groove binding mode and the hydrophobic cavity located in subdomain IIA of HSA with the binding constant of 4.144 × 105 M[Formula: see text] and [Formula: see text] 106 M[Formula: see text], respectively. Thermodynamic parameters revealed that both DNA- and HSA binding were spontaneous process. The main driven forces were the hydrogen bond and van der Waals for the former, but hydrophobic interaction for the latter, which were further confirmed by molecular docking modeling. Manganese [Formula: see text]-confused porphyrin 1 could cleave the supercoiled plasmid DNA efficiently in the presence of hydrogen peroxide. Hydroxyl radical ([Formula: see text]OH) was found the active species for oxidative damage of DNA.

Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA

Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 10(4)Lmol(-1), and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.

meso-Mono-[4-(1,4,7-triazacyclononanyl)]-tri(phenyl)]porphyrin and the respective zinc(ii)-complex: complete characterization and biomolecules binding abilities

We aimed to synthesize a new series of triazacyclononanyl-porphyrins (4and5) with the potential ability to bind DNA.

DNA Binding, Photonuclease Activity and Human Serum Albumin Interaction of a Water-Soluble Freebase Carboxyl Corrole

The DNA binding property of 5,10,15-Tris(4-carboxyphenyl) corrole (TCPC) was studied by UV-Visible, fluorescence and circular dichroism (CD) spectroscopic methods. TCPC can bind to ct-DNA via an outside binding mode with the binding constant of K_b = 1.05 × 10⁵ M⁻¹. TCPC also displayed good photonuclease activity, which involves singlet oxygen species (¹O₂). The binding constant between TCPC and human serum albumin (HSA) is K_A = 2.24 × 10⁵ M⁻¹ with a simulated binding distance of 2.06 nm. The fluorescence quenching of HSA by TCPC followed a static quenching process. Site marker competitive displacement experiments indicated that warfarin site I is the main binding site. The secondary structure of HSA was changed upon interaction with TCPC, which was confirmed by UV-Visible and CD spectroscopy.

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.

Synthesis, characterization and biomolecule-binding properties of novel tetra-platinum(ii)-thiopyridylporphyrins

New tetra-platinum(ii)-thiopyridylporphyrin complexes and their DNA binding studies.

Synthesis and characterization of Co(ii) and Fe(ii) peptide conjugates as hydrolytic cleaving agents and their preferential enantiomeric disposition for CT-DNA: structural investigation of l-enantiomers by DFT and molecular docking studies

Molecular docked model of Co(ii) peptide conjugate with DNA and the mechanism of hydrolytic cleavage of pBR322 DNA.

Comparative study of the interaction of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP) in its free base and Fe derivative form with oligo(dA.dT)15 and oligo(dG.dC)15

Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Followings are the observed changes in the spectral properties of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP), as a free-base porphyrin with no axial ligand, and its Fe derivative (FeTMAP) upon interaction with oligo(dA.dT)15 and oligo(dG.dC)15: (1) the substantial red shift and hypochromicity at the Soret maximum in the UV-vis spectra; (2) the increased RLS intensity by increasing the ionic strength; and (3) an intense bisignate excitonic CD signal. All of them are the reasons for TMAP and FeTMAP binding to oligo(dA.dT)15 and oligo(dG.dC)15 with the outside binding mode, accompanied by the self-stacking of the ligands along the oligonucleotide helix. The CD results demonstrated a drastic change from excitonic in monomeric behavior at higher ionic strengths, which indicates the groove binding of the ligands with oligonucleotides. Molecular docking also confirmed the groove binding mode of the ligands and estimated the binding constants and energies of the interactions. Their interaction trend was further confirmed by molecular dynamics technique and structure parameters obtained from simulation. It showed that TMAP reduced the number of intermolecular hydrogen bonds and increased the solvent accessible surface area in the oligonucleotide. The self-aggregation of ligands at lower concentrations was also confirmed.

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.

Mechanism of DNA Strand Cleavage Induced by Hexaaza Macrocyclic Nickel (II) Complex

The hexaaza macrocyclic nickel(II) complex (Ni(II)L-1,8-Dihydroxyethyl-1,3,6,8,10,13-hexaazacyclotetradecane nickle(II) perchlorate monohydrate) was synthesized and purified. The electrochemical character of Ni(II)L was measured, and the interaction of Ni(II)L with calf thymus DNA (CT-DNA) was studied using electrochemical techniques, emission and viscometry, and circular dichroic spectral measurements. All of the experiments suggested that the complex interacted with DNA primarily by partial intercalation. The cyclic voltammetry (CV) showed that the currents of both the reduction peak and the oxidation peak decreased significantly in the presence of DNA, which indicated that Ni(II)L could interact with DNA. The fluorescence intensity of the DNA-ethidium bromide(EB) system decreased distinctly when Ni(II)L was added. The results indicated that Ni(II)L may be completed effectively with EB for the intercalative binding sites. The viscosity of DNA would be decreased slightly by the addition of the complex. Circular dichroic spectral studies revealed that B conformation of CT-DNA became more A-like in structure on interaction with the complex. Noticeably, the complex has been found to cleave plasmid pBR 322 by agarose gel electrophoresis and cleave CT-DNA by high-performance liquid chromatography (HPLC).

3,6-bis(3-alkylguanidino)acridines as DNA-intercalating antitumor agents

A series of 3,6-bis(3-alkylguanidino) acridines was prepared and the interaction of these novel compounds with calf thymus DNA was investigated with UV-vis, fluorescence and circular dichroism spectroscopy, in addition to DNA melting techniques. The binding constants K were estimated to range from 1.25 to 5.26 × 10(5) M(-1), and the percentage of hypochromism was found to be 17-42% (from spectral titration). UV-vis, fluorescence and circular dichroism measurements indicated that the compounds act as effective DNA-intercalating agents. Electrophoretic separation proved that ligands 6a-e relaxed topoisomerase I at a concentration of 60 μM, although only those with longer alkyl chains were able to penetrate cell membranes and suppress cell proliferation effectively. The biological activity of novel compounds was assessed using different techniques (cell cycle distribution, phosphatidylserine externalization, caspase-3 activation, changes in mitochondrial membrane potential) and demonstrated mostly transient cytostatic action of the ethyl 6c and pentyl 6d derivatives. The hexyl derivative 6e proved to be the most cytotoxic. Different patterns of cell penetration were also observed for individual derivatives. Principles of molecular dynamics were applied to explore DNA-ligand interactions at the molecular level.

Porphyrins bearing quaternary azaaromatic moieties

In this review, porphyrins bearing quaternary azaaromatic moieties are described as follows: firstly those with useful physicochemical properties, then, species showing biological activities and finally, porphyrins bound with fullerenes and with cyclodextrins.

A study on the self assembly of Fe(II) and dual binding of Ni(II) porphyrazines on CT-DNA

Interaction of N , N ′, N ″, N ‴-tetramethyltetra-2,3-pyridinoporphyrazinatonickel(II), ([ Ni (2,3- tmtppa )]4+) and N , N ′, N ″, N ‴-tetramethyltetra-2,3-pyridinoporphyrazinatoiron(II), ([ Fe (2,3- tmtppa )]4+) with calf thymus DNA (CT-DNA) have been studied in 1mM phosphate buffer and low ionic strength (5 mM NaCl ) using several spectroscopic techniques: absorbance, fluorescence and circular dichroism. The 2:1 porphyrazine/DNA mole ratio, existence of moderate hypochromicity, moderate and progressive red shift and conservative ICD in the visible part of [ Fe (2,3- tmtppa )]4+ spectra suggested an outside binding with self-stacking mode. Analysis of the dramatic hypochromicity, small blue shift and bisignate ICD in the Q-band absorption region of [ Ni (2,3- tmtppa )]4+ spectra and 1:1 porphyrazine/DNA mole ratio possibly led us to the dual binding mode of this complex, i.e. at the minor and major grooves of DNA. The influence of the ionic strength on the porphyrazine-DNA binding confirmed this suggestion. The fluorescence quenching of DNA-ethidium bromide complex by porphyrazines was investigated. The values of quenching constants ( K sv ) and the rate constants of the quenching ( K q ) were determined by Stern-Volmer equation. The values of K sv have been obtained (2.07 ± 0.11) × 106 and (0.48 ± 0.01) × 106 M−1 for [ Fe (2,3- tmtppa )]4+ and [ Ni (2,3- tmtppa )]4+, respectively, at 27°C. The higher affinity of [ Fe (2,3- tmtppa )]4+ for the quenching of EB-DNA fluorescence with respect to Ni complex was attributed to self-stacking of the former along DNA helix and favorable energy transfer between EB+ and cationic porphyrazine. ΔG25 (the difference between the free energy of the native ( N ) and the denatured (D) form of DNA at 25°C), ΔHm and ΔSm (difference between enthalpy and entropy at Tm) were extracted from thermal curves. The decline in the melting temperature of DNA following the addition of porphyrazine complexes confirms that the substantial mode of Ni and Fe interaction is not intercalation. The thermodynamic results imply that both Ni and Fe complexes have a slight destabilizing effect on the DNA. A comparison between [ Ni ( tmtppa )]4+ and [ Fe ( tmtppa )]4+ indicates that the latter is more effective than the former.

Experimental and DFT studies on DNA binding and photocleavage of two cationic porphyrins. Effects of the introduction of a carboxyphenyl into pyridinium porphyrin

The DNA-binding affinities and DNA photocleavage abilities of cationic porphyrin, 5-(4-carboxyphenyl)-10,15,20-tris(4-methylpyridiniumyl)porphyrin (CTMPyP), and its reference compound meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin (H2TMPyP) have been investigated. The DNA-binding behaviors of the two compounds in NaH2PO4 buffer were compared systematically by using absorption, fluorescence and circular dichroism (CD) spectra, thermal denaturation as well as viscosity measurements. The experimental results show that CTMPyP binds to DNA in an outside binding mode, while H2TMPyP in an intercalative mode. Photocleavage experiments reveal that both two compounds employ 1O2-mediated mechanism in cleaving DNA and H2TMPyP can cleave DNA more efficiently than CTMPyP. Theoretical calculations were carried out with the density functional theory (DFT), and the calculated results indicate that the character and energies of some frontier orbitals of CTMPyP are quite different from those of H2TMPyP. These theoretical results can be used to explain their different DNA-binding modes and affinities to a certain extent.

Study on the interaction of 5-pyridine-10,15,20-tris-(p-chlorophenyl)porphyrin with cyclodextrins and DNA by spectroscopy

The interaction of 5-pyridine-10,15,20-tris-(p-chlorophenyl)porphyrin (PyTPP) with beta-CD and TM-beta-CD were examined by UV-vis absorption, fluorescence and (1)H NMR spectroscopy. PyTPP prefers to form the 1:1 inclusion complex with TM-beta-CD but hardly form inclusion complex with beta-CD. An inclusion constant (K) for the formation of PyTPP-TM-beta-CD inclusion complex has been evaluated to be 4.4x10(3)L/mol from the absorbance changes. This K value is nearly the same as that 4.5x10(3)L/mol obtained from the fluorescence intensity changes. Compared to beta-CD, the inclusion ability of TM-beta-CD with PyTPP is stronger. It indicates that the hydrophobic effect plays an important role in the inclusion procedure. The mechanism of inclusion interaction was carried out by 1H NMR technique. Furthermore, the interaction of PyTPP with DNA is shown here. It can bind DNA by out-side stacking along the DNA helix but not by intercalation because of the high electron density in the porphyrin core. The binding constant and binding number of PyTPP to DNA are 4.3x10(3) and 1.3, respectively. The interaction of PyTPP with DNA was further carried out in the presence of TM-beta-CD. The significant decrease of the binding constant and binding number were observed and the interaction of porphyrin-bound DNA has been inhibited, which was due to the fact that PyTPP inter into the cavity of TM-beta-CD and influence binding affinity of PyTPP to DNA.

Cellular pharmacological properties of gold(III) porphyrin 1a, a potential anticancer drug lead

The development of gold(III) complexes as potential anticancer drugs with higher cytotoxicity and fewer side effects than existing metal anticancer drugs has been actively pursued in recent years. In this study, we explored the cellular pharmacological properties of gold(III) porphyrin 1a, an anticancer drug lead we previously described. The cytotoxicity study of gold(III) porphyrin 1a by naphthol blue black (NBB) staining assay demonstrated that the higher cytotoxicity of gold(III) porphyrin 1a was not related to its photosensitizing activity. Serum dependent test revealed that serum proteins exhibited lesser effects on the activity of gold(III) porphyrin 1a. In addition, in vivo and in vitro binding assays showed that gold(III) porphyrin 1a acted on DNA noncovalently, which was differently from cisplatin. Flow cytometric study indicated that gold(III) porphyrin 1a inhibited cell growth partly through abrogating cell cycle at G(0)-G(1), and induced apoptosis in SUNE1 cells. The enhanced expression of p53, a cell cycle-controlling and apoptosis-related protein, further demonstrated that the cell cycle arrest and apoptosis induced by gold porphyrin 1a were p53 dependent. Our results highlighted the potential of gold(III) porphyrin 1a as an anticancer drug.