Interaction of Cationic Nickel and Manganese Porphyrins with the Minor Groove of DNA

Interactions of Mn complexes with DNA: the relevance of therapeutic applications towards cancer treatment

Manganese (Mn) is one of the most significant bio-metals that helps the body to form connective tissue, bones, blood clotting factors, and sex hormones. It is necessary for fat and carbohydrate metabolism, calcium absorption, blood sugar regulation, and normal brain and nerve functions. It accelerates the synthesis of proteins, vitamin C, and vitamin B. It is also involved in the catalysis of hematopoiesis, regulation of the endocrine level, and improvement of immune function. Again, Mn metalloenzymes like arginase, glutamine synthetase, phosphoenolpyruvate decarboxylase, and Mn superoxide dismutase (MnSOD) contribute to the metabolism processes and reduce oxidative stress against free radicals. Recent investigations have revealed that synthetic Mn-complexes act as antibacterial and antifungal agents. As a result, chemists and biologists have been actively involved in developing Mn-based drugs for the treatment of various diseases including cancer. Therefore, any therapeutic drugs based on manganese complexes would be invaluable for the treatment of cancer/infectious diseases and could be a better substitute for cisplatin and other related platinum based chemotherapeutic drugs. From this perspective, attempts have been made to discuss the interactions and nuclease activities of Mn(II/III/IV) complexes with DNA through which one can evaluate their therapeutic applications.

DNA-Interactive and Damage Study with meso-Tetra(2-thienyl)porphyrins Coordinated with Polypyridyl Pd(II) and Pt(II) Complexes

We report the DNA-binding properties of three porphyrins with peripheral thienyl substituents (TThPor, PdTThPor and PtTThPor). The binding capacity of each porphyrin with DNA was determined by UV-Vis and steady-state fluorescence emission spectroscopy combined with molecular docking calculations. The results suggest that the interaction of these compounds probably occurs via secondary interactions via external grooves (minor grooves) around the DNA macromolecule. Moreover, porphyrins containing peripheral Pd(II) or Pt(II) complexes (PdTThPor and PtTThPor) were able to promote photo-damage in the DNA.

Gold(III) porphyrins: Synthesis and interaction with G-quadruplex DNA

G-quadruplex nucleic acids (G4s) are RNA and DNA secondary structures involved in the regulation of multiple key biological processes. They can be found in telomeres, oncogene promoters, RNAs, but also in viral genomes. Due to their unique structural features, very distinct from the canonical duplexes or single-strands, G4s represent promising pharmacological targets for small molecules, namely G4-ligands. Gold(III) penta-cationic porphyrins, as specific G4 ligands, are able to inhibit HIV-1 infectivity and their antiviral activity correlates with their affinity for G4s. Up to now, one of the best antiviral compounds is meso-5,10,15,20-tetrakis[4-(N-methyl-pyridinium-2-yl)phenyl]porphyrinato gold(III) (1). Starting from this compound, we report a structure/affinity relationship study of gold(III) cationic porphyrins to find out the best porphyrin candidate for functionalization, in order to study the antiviral mechanism of action of these gold(III) porphyrins.

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.

Reactivity and Stability of Metalloporphyrin Complex Formation: DFT and Experimental Study

The interaction of three cationic porphyrins—meso-tetrakis (N-methylpyridinium-4-yl) porphyrin (TMPyP), meso-tetrakis (1,3-dimethylimidazolium-2-yl) porphyrin (TDMImP), and meso-tetrakis (1,2-dimethylpyrazolium-4-yl) porphyrin (TDMPzP)—with five heavy metals was studied computationally, and binding constants were calculated based on data obtained by an experimental method and compared. The reactivity and stability of their complexes formed with lead, cadmium, mercury, tin, and arsenic ions were observed in DFT global chemical reactivity descriptors: the electronic chemical potential (µ), chemical hardness (η), and electrophilicity (ω). The results show that M-TDMPzP has higher chemical hardness and lower electrophilicity compared to M-TMPyP and M-TDMImP, indicating the reaction of TDMPzP with metals will form a more stable complex. Specifically, Cd-TDMPzP complexes can stabilize the system, with a lower energy and electronic chemical potential, higher chemical hardness, smaller electrophilicity, and higher binding constant value compared to Pb-TDMPzP and Hg-TDMPzP. This result suggests that the interaction of the Cd²⁺ ion with TDMPzP will produce a stable complex.

G-Quadruplex binding optimization by gold(iii) insertion into the center of a porphyrin

Porphyrins represent a valuable class of ligands for G-quadruplex nucleic acids. Herein, we evaluate the binding of cationic porphyrins metallated with gold(iii) to G-quadruplex DNA and we compare it with other porphyrin derivatives. The G-quadruplex stabilization capacity and the selectivity of the various porphyrins were evaluated by biophysical and biochemical assays. The porphyrins were also tested as inhibitors of telomerase. It clearly appeared that the insertion of gold(iii) ion in the center of the porphyrin increases the binding affinity of the porphyrin for the G-quadruplex target. Together with modelling studies, it is possible to propose that the insertion of the square planar gold(iii) ion adds an extra positive charge on the complex and decreases the electron density in the porphyrin aromatic macrocycle, both properties being in favour of stronger electrostatic and π-staking interactions.

Catalytic antioxidants for therapeutic medicine

In this Review, we focus on catalytic antioxidant study based on transition metal complexes, organoselenium compounds, supramolecules and protein scaffolds.

Influence of the SPR Experimental Conditions on the G-Quadruplex DNA Recognition by Porphyrin Derivatives

Surface plasmon resonance (SPR) is a powerful technique to study the interactions of ligands with analytes and therefore a number of biosensor surfaces and injection methods have been developed so far. However, many experimental parameters can affect the interactions and consequently the affinity measurements. In particular, the interactions of positively charged analytes (often used for anionic nucleic acids targets) can be influenced by the sensing surfaces (e.g., negatively charged), leading to significant nonspecific interactions as well as regeneration problems. The aim of the present work is to investigate the effect of different parameters, including ionic strength, SPR biosensor (i.e., nature of the surfaces), and the injection method on the recognition of porphyrin G-quadruplex ligands. We demonstrate that the injection method does not influence the affinity whereas the ionic strength and the nature of the surface impact the recognition properties of the porphyrin for the G-quadruplex DNA. We also found that self-assembled monolayer coating surface presents many advantages in comparison with carboxymethylated dextran surface for SPR studies of G-quadruplex DNA/ligand interactions: (i) the electrostatic interaction with charged analytes is less important, (ii) its structure/composition is less sensitive to the ionic concentration and less prone to unspecific adsorption, (iii) it is easily homemade, and (iv) the cost is approximately 10 times cheaper.

Comparative study of binding interactions between porphyrin systems and aromatic compounds of biological importance by multiple spectroscopic techniques: A review

The specific spectroscopic and redox properties of porphyrins predestine them to fulfill the role of sensors during interacting with different biologically active substances. Monitoring of binding interactions in the systems porphyrin-biologically active compound is a key question not only in the field of physiological functions of living organisms, but also in environmental protection, notably in the light of the rapidly growing drug consumption and concurrently the production of drug effluents. Not always beneficial action of drugs on natural porphyrin systems induces to further studies, with commercially available porphyrins as the model systems. Therefore the binding process between several water-soluble porphyrins and a series of biologically active compounds (e.g. caffeine, guanine, theophylline, theobromine, xanthine, uric acid) has been studied in different aqueous solutions analyzing their absorption and steady-state fluorescence spectra, the porphyrin fluorescence lifetimes and their quantum yields. The magnitude of the binding and fluorescence quenching constants values for particular quenchers decreases in a series: uric acid > guanine > caffeine > theophylline > theobromine > xanthine. In all the systems studied there are characters of static quenching, as a consequence of the π-π-stacked non-covalent and non-fluorescent complexes formation between porphyrins and interacting compounds, accompanied simultaneously by the additional specific binding interactions. The porphyrin fluorescence quenching can be explain by the photoinduced intermolecular electron transfer from aromatic compound to the center of the porphyrin molecule, playing the role of the binding site. Presented results can be valuable for designing of new fluorescent porphyrin chemosensors or monitoring of drug traces in aqueous solutions. The obtained outcomes have also the toxicological and medical importance, providing insight into the interactions of the water-soluble porphyrins with biologically active substances.

New class of artificial enzyme composed of Mn-porphyrin, imidazole, and cucurbit[10]uril toward use as a therapeutic antioxidant

In this study, we investigated a new class of artificial enzymes composed of Mn-porphyrin, imidazole, and cucurbit[10]uril (CB[10]) toward therapeutic antioxidants.

A selective distance-based paper analytical device for copper(II) determination using a porphyrin derivative

Meso-tetrakis(1,2-dimethylpyrazolium-4-yl)porphyrin sulfonate (TDMPzP), a water-soluble porphyrin derivative, was synthesized and used as a colorimetric reagent for Cu²⁺ detection on a microfluidic paper-based analytical device (µPAD) using distance-based quantification. TDMPzP showed a high selectivity for Cu²⁺ detection in aqueous solutions. When Cu²⁺ was added to the TDMPzP under acidic conditions, a color change from green to a pink was observed by the naked eye. Under optimized conditions, the application of this system to a distance-based μPAD exhibited good analytical response. The presence of common metal ions (Al³⁺, Fe³⁺, Mg²⁺, Co²⁺, Mn²⁺, Zn²⁺, Pb²⁺, Cd²⁺, Sn²⁺, and Ni²⁺) did not interfere with Cu²⁺ detection within reasonable tolerance ratios. The lowest concentration of copper that could be measured was 1mgL^-1 (1ppm) which meets the requirements for drinking water contamination regulations from the US Environmental Protection Agency (EPA) and World Health Organization (WHO) guidelines for drinking water. Real drinking water samples were analyzed to confirm the practical application of this system and the results showed good agreement with ICP-MS data. This distance-based µPAD based on TDMPzP for Cu²⁺ detection is convenient and effective for real-time drinking water analysis.

The pKa value of the proximal water molecule trans to a high-valent MnVO porphyrin: towards the control of reactivity by pH

In water, the protonation state of the proximal water molecule of a high-valent manganese-oxo porphyrin could be controlled by pH. While in interaction with DNA the porphyrin was able to cleave DNA, only when the proximal water molecule was in the form of a hydroxyl group.

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.

Cationic Porphyrin-Anionic Surfactant Mixtures for the Promotion of Self-Organized 1:4 Ion Pairs in Water with Strong Aggregation Properties

We performed a systematic study on the spectroscopic and aggregation properties of stoichiometric mixtures (1:4) of the tetracationic meso-tetrakis(4-N-methylpyridinium)porphyrin (H2 TMPyP) and three sodium alkylsulfate surfactants (tetradecyl, hexadecyl, and octadecylsulfate) in an aqueous solution. The objective was to build a supramolecular aggregate, which would favor the internalization of tetracationic porphyrins in cells without chemical modification of the structure of the porphyrin. We show that stoichiometric H2 TMPyP/alkylsulfate (1:4) mixtures lead to the formation of large hollow spherical aggregates (60-160 nm). The TEM images show that the membrane of these aggregates are composed of smaller aggregates, which are probably rod-like micelles. These rod-like micelles have a hydrophobic core composed of the alkyl chains of the alkylsulfate surfactant, whereas the charged surface corresponds to the tetracationic porphyrins.

Cobalt(III)porphyrin to target G-quadruplex DNA

G-quadruplex DNA ligands attract much attention because of their potential use in biology. Indeed they may interfere with G-quadrulex nucleic acid function in cells. Most of the G-quadruplex ligands so far reported (including also metal complexes) are large planar aromatic compounds that interact by π-π stacking with an external G-quartet of quadruplex. Porphyrins are well-known G-quadruplex ligands. We report herein a new porphyrin scaffold (meso-tetrakis(4-(N-methyl-pyridinium-2-yl)phenyl)porphyrin) able to strongly and selectively bind to G-quadruplex DNA. We show that even when this porphyrin is metallated with cobalt(III), i.e. it carries two water molecules as axial ligands on the cobalt ion, on each face of the porphyrin, the interaction occurs by a π-stacking-like mode with an external G-quartet of quadruplex DNA.

Chemiluminescence detection of a protein through the aptamer-controlled catalysis of a porphyrin probe

Sensitive and selective protein detection based on the aptamer-controlled noncovalent porphyrin probe self-assembly is reported for the first time. Vascular endothelial growth factor (VEGF) is a predominant biomarker in cancer angiogenesis. In this work, a positively charged porphyrin probe, manganese(III) meso-tetrakis(N-methylpyridinum-4-yl)porphyrin (Mn-PyP), was prepared. Using it as a catalyst, a label-free chemiluminescence (CL) turn-on approach for sensitive VEGF detection is developed. Mn-PyP could catalyze the luminol CL reaction. The VEGF aptamer could induce aggregation of Mn-PyP. As a result, the Mn-PyP-catalyzed CL reaction is efficiently suppressed. Upon the addition of VEGF, the specific binding of VEGF to the aptamer weakens the interactions between the aptamer and Mn-PyP. The Mn-PyP monomers are released, and a turn-on CL signal is thus detected. Our method is quite sensitive; 50 pM of VEGF could be easily detected. It is also very selective against other proteins. Our assay provides an aptamer-based efficient way for protein quantification.

Formation of the carboxamidine precursor of cyanuric acid from guanine oxidative lesion dehydro-guanidinohydantoin

DNA damage under oxidative stress leads to oxidation of guanine base. The identification of the resulting guanine lesions in cellular DNA is difficult due to the sensitivity of the primary oxidation products to hydrolysis and/or further oxidation. We isolated dehydroguanidino-hydantoin (DGh) (or oxidized guanidinohydantoin), a secondary oxidation product of guanine, and showed that this lesion reacts readily with nucleophiles such as asymmetric peroxides and transforms to 2,4,6-trioxo-1,3,5-triazinane-1-carboxamidine residue. Further hydrolysis of this intermediate leads to cyanuric acid and finally to urea residue. This work demonstrates a new possible pathway for the formation of the well-known carboxamidine precursor of cyanuric acid lesion.

Metal-mediated DNA damage and cell death: mechanisms, detection methods, and cellular consequences

Metal ions cause various types of DNA damage by multiple mechanisms, and this damage is a primary cause of cell death and disease.

A single nuclease-resistant linkage in DNA as a versatile tool for the characterization of DNA lesions: application to the guanine oxidative lesion "G+34" generated by metalloporphyrin/KHSO(5) reagent

The oxidation of an oligonucleotide containing a single nuclease-resistant phosphodiester link, a stereoisomerically pure methylphosphonate, by manganese (Mn-TMPyP) or iron (Fe-TMPyP) porphyrin associated to KHSO(5) allowed the isolation and characterization of a guanine lesion corresponding to an increase of mass of 34 amu as compared to guanine ("G+34"), namely, 5-carboxamido-5-formamido-2-iminohydantoin. Enzymatic digestion of the damaged oligonucleotide afforded, apart from the undamaged nucleotide monomer pool, a unique dinucleotide doubly modified with a methylphosphonate and an oxidized guanine base that is suitable for NMR analysis. The method can be applied to the study of any DNA lesion. More importantly, the method can be extended to the analysis of DNA damage in a sequence context. Any preselected residue in a DNA sequence may be individually analyzed by the easy introduction of a single nuclease-resistant link at the 3'- or 5'-position.

Improvement of porphyrins for G-quadruplex DNA targeting

G-quadruplex nucleic acids are emerging as therapeutic targets for small molecules referred to as small-molecule G-quadruplex ligands. The porphyrin H(2)-TMPyP4 was early reported to be a suitable motif for G-quadruplex DNA recognition. It probably binds to G-quadruplex nucleic acid through π-π stacking with the external G-quartets. We explored chemical modifications of this porphyrin such as insertion of various metal ions in the centre of the aromatic core and addition of bulky substituents that may improve the specificity of the compound toward G-quadruplex DNA. Porphyrin metallation, affording a G4-ligand with two symmetric faces, allowed the conclusion that the presence of an axial water molecule perpendicular to the aromatic plane lowered but did not hamper π-π stacking interactions between the aromatic parts of the ligand on the one hand and the external G-quartet on the other. The charge introduced in the centre of the porphyrin had little influence on binding. Thus, the ionic channel in the centre of G-quadruplex nucleic acids was not found to provide clear additional molecular clues for G-quadruplex nucleic acids targeting by porphyrins tested in the present study. Furthermore, we confirmed the unique G-quadruplex selectivity of a porphyrin modified with four bulky substituents at the meso positions and showed that although the compound is not "drug-like" it was capable of entering cells in culture and mediated some of the typical cellular effects of small-molecule G-quadruplex ligands.