Multiplicity of metal ion binding patterns to nucleobases

A Multistep Oxidative Cascade Reaction from a Naphthalenediol-Based Pre-Ligand to a Tetranuclear Perylenequinone-Based FeIII Complex

We have developed a family of dinuclear complexes using 2,7-disubstituted 1,8-naphthalenediol ligands that bind by molecular recognition to two neighboring phosphate diesters of the DNA backbone with the dinuclear CuII and NiII complexes exhibiting a severe cytotoxicity for human cancer cells. To increase the binding affinity, we intended to synthesize the corresponding dinuclear FeIII complex. Surprisingly, we obtained a tetranuclear FeIII perylene-based complex instead of the expected dinuclear FeIII naphthalene-based complex. In order to establish a rational and reproducible synthesis, we carefully analyzed this reaction. This revealed a multistep oxidative cascade reaction including the pre-coordination of FeII ions in the N3-binding pockets, the Lewis-acid assisted MOM-deprotection of the pre-ligand by the pre-oriented FeII ions, two oxidative aromatic C-C coupling reactions, oxidation of the perylene-based backbone and of FeII to FeIII. The careful analysis of bond lengths, HOMA indices (harmonic oscillation model of aromaticity), FTIR and UV-Vis-NIR spectra supported by DFT calculations reveals the presence of an aromatic 18-electron oxidized perylenequinone ligand backbone. In summary, a multistep cascade reaction involving in total a 10-electron oxidation has been established for the straight-forward synthesis of an unprecedented perylenequinone-based ligand system.

Structural Effect of N-7 Alkylation in 6-Chloropurine on Cu (II) Binding: Effect of Anions and Magnetic Studies

This study investigates the anion-directed assembly of discrete copper (II) complexes. The ligands of choice are two N7-alkyl-purine-based neutral ligands. These ligands facilitate the exclusive coordination through the N3 and N9 positions, preventing polymeric chain formation. Perchlorate ions promoted the formation of discrete paddlewheel-like complexes with the general formula [Cu2(μ-Pur)4(CH3CN)2]4+, while chloride ions yielded chloride-bridged dimers of the form [Cu2(Pur)2(μ-Cl)2Cl2]. Copper-copper bond distances within these complexes ranged from 2.92 to 2.98 Å. Magnetic susceptibility measurement of chloride-bridged complexes exhibited antiferromagnetic coupling, whereas paddlewheel complexes displayed more complex alternating ferromagnetic and antiferromagnetic interactions. Chloride-bridged compounds exhibited strong near-infrared absorption.

Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution

Phosphate derivatives and their interaction with metal cations are involved in many important biological phenomena, so an accurate characterization of the phosphate-metal interaction is necessary to properly understand the role of phosphate-metal contacts in mediating biological function. Herein, we improved the standard 12-6 Lennard-Jones (LJ) potential via the usage of the 12-6-4 LJ model, which incorporates ion-induced dipole interactions. Via parameter scanning, we fine-tuned the 12-6-4 LJ polarizability values to obtain accurate absolute binding free energies for the phosphate anions H2PO4-, HPO42-, PO43- coordinating with Ca2+ and Mg2+. First, we modified the phosphate 12-6-4 LJ parameters to reproduce the solvation free energies of the series of phosphate anions using the thermodynamic integration (TI) method. Then, using the potential mean force (PMF) method, the polarizability of the metal-phosphate interaction was obtained. We show that the free energy profiles of phosphate ions coordinated to Ca2+ and Mg2+ generally show similar trends at longer metal-phosphate distances, while the absolute binding energy values increased with deprotonation. The resulting parameters demonstrate the flexibility of the 12-6-4 LJ-type nonbonded model and its usefulness in accurately describing cation-anion interactions.

Synthesis and Characterization of Zn(II) Complex of 4-chloro-2-(((2-phenoxyphenyl)imino)methyl)phenol and its Biological Efficacies: DNA Interaction, ADMET, DFT and Molecular Docking Study

Condensing 2-phenoxyaniline with 5-chlorosalicyldehyde under reflux conditions, a 4-chloro-2-(((2-phenoxyphenyl)imino)methyl)phenol Schiff base has been Synthesized. A zinc complex was synthesized by combining the ligand in a 1:1 molar ratio with zinc sulphateheptahydrate. Mass spectroscopy, NMR, infrared, and elemental analysis were used to characterize the ligand and zinc complex. By measuring the molar conductance, the non-electrolytic character of the complex was confirmed. The zinc ion is coordinated in a pentadentate manner, according to an IR and NMR investigation. Viscosity measurements, absorption and fluorescence spectroscopy were utilized to examine the complex's interaction with CT (calf thymus) DNA. Furthermore, the ligand and complex's ADMET characteristics were ascertained through the use of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) study. Calculation of the different electronic parameters of the optimized structure through Density Functional Theory (DFT) indicated the stability of the Zn(II) complex. Molecular docking study reflected the future opportunity for the consideration of Zn(II) complex to fight against Alzheimer and Glaucoma diseases.

Synthesis and crystal structure of a silver(I) 6-methylmercaptopurine riboside complex

Silver nitrate reacts with 6-methylmercaptopurine riboside (6-MMPR) in aqueous solution containing methanol and dimethyl sulfoxide at room temperature to give a colourless crystalline complex, namely, bis(6-methylmercaptopurine riboside-κN7)(nitrato-κ2O,O')silver(I) 2.32-hydrate, [Ag(NO3)(C11H14N4O4S)2]·2.32H2O. The crystal structure, determined from synchrotron diffraction data, shows a central AgI ion on a crystallographic twofold rotation axis, coordinated in an almost linear fashion by two 6-MMPR ligands via atom N7 (purine numbering), with the nitrate counter-ion loosely coordinated as a bidentate ligand, forming a discrete molecular complex as an approximate dihydrate. The complex and water molecules are connected in a three-dimensional network by hydrogen bonding.

Hydrogen-Bonding Interactions from Nucleobase-Decorated Supramolecular Polymer: Synthesis, Self-Assembly and Biomedical Applications

The fabrication of supramolecular materials for biomedical applications such as drug delivery, bioimaging, wound-dressing, adhesion materials, photodynamic/photothermal therapy, infection control (as antibacterial), etc. has grown tremendously, due to their unique properties, especially the formation of hydrogen bonding. Nevertheless, void space in the integration process, lack of feasibility in the construction of supramolecular materials of natural origin in living biological systems, potential toxicity, the need for complex synthesis protocols, and costly production process limits the actual application of nanomaterials for advanced biomedical applications. On the other hand, hydrogen bonding from nucleobases is one of the strategies that shed light on the blurred deployment of nanomaterials in medical applications, given the increasing reports of supramolecular polymers that promote advanced technologies. Herein, we review the extensive body of literature about supramolecular functional biomaterials based on nucleobase hydrogen bonding pertinent to different biomedical applications. It focuses on the fundamental understanding about the synthesis, nucleobase-decorated supramolecular architecture, and novel properties with special emphasis on the recent developments in the assembly of nanostructures via hydrogen-bonding interactions of nucleobase. Moreover, the challenges, plausible solutions, and prospects of the so-called hydrogen bonding interaction from nucleobase for the fabrication of functional biomaterials are outlined.

Ru-Controlled Thymine Tautomerization Frozen by a k1(O)-, k2(N,O)-Metallacycle: An Experimental and Theoretical Approach

The reaction of mer-(Ru(H)₂(CO)(PPh₃)₃) (1) with one equivalent of thymine acetic acid (THAcH) unexpectedly produces the macrocyclic dimer k¹(O), k²(N,O)-(Ru(CO)(PPh₃)₂THAc)₂ (4) and, concomitantly, the doubly coordinated species k¹(O), k²(O,O)-(Ru(CO)(PPh₃)₂THAc) (5). The reaction promptly forms a complicated mixture of Ru-coordinated mononuclear species. With the aim of shedding some light in this context, two plausible reaction paths were proposed by attributing the isolated or spectroscopically intercepted intermediates on the basis of DFT-calculated energetic considerations. The cleavage of the sterically demanding equatorial phosphine in the mer-species releases enough energy to enable self-aggregation, producing the stable, symmetric 14-membered binuclear macrocycle of 4. The k¹-acetate iminol (C=N-OH) unit of the mer-tautomer k¹(O)-(Ru(CO)(PPh₃)₂(THAc)) (2) likely exhibits a stronger nucleophilic aptitude than the prevalent N(H)-C(O) amido species, thus accomplishing extra stabilization through concomitant k²(N,O)-thymine heteroleptic side-chelation. Furthermore, both the ESI-Ms and IR simulation spectra validated the related dimeric arrangement in solution, in agreement with the X-ray determination of the structure. The latter showed tautomerization to the iminol form. The ¹H NMR spectra in chlorinated solvents of the kinetic mixture showed the simultaneous presence of 4 and the doubly coordinated 5, in rather similar amounts. THAcH added in excess preferentially reacts with 2 or trans-k²(O,O)-(RuH(CO)(PPh₃)₂THAc) (3) rather than attacking the starting Complex 1, promptly forming the species of 5. The proposed reaction paths were inferred by spectroscopically monitoring the intermediate species, for which the results were strongly dependent on the of conditions the reaction (stoichiometry, solvent polarity, time, and the concentration of the mixture). The selected mechanism proved to be more reliable, due to the final dimeric product stereochemistry.

Hybrid Hydrogen-Bonded Organic Frameworks: Structures and Functional Applications

As a new class of porous crystalline materials, hydrogen-bonded organic frameworks (HOFs) assembled from building blocks by hydrogen bonds have gained increasing attention. HOFs benefit from advantages including mild synthesis, easy purification, and good recyclability. However, some HOFs transform into unstable frameworks after desolvation, which hinders their further applications. Nowadays, the main challenges of developing HOFs lie in stability improvement, porosity establishment, and functionalization. Recently, more and more stable and permanently porous HOFs have been reported. Of all these design strategies, stronger charge-assisted hydrogen bonds and coordination bonds have been proven to be effective for developing stable, porous, and functional solids called hybrid HOFs, including ionic and metallized HOFs. This Review discusses the rational design synthesis principles of hybrid HOFs and their cutting-edge applications in selective inclusion, proton conduction, gas separation, catalysis and so forth.

Developing Metal-Binding Isosteres of 8-Hydroxyquinoline as Metalloenzyme Inhibitor Scaffolds

The use of metal-binding pharmacophores (MBPs) in fragment-based drug discovery has proven effective for targeted metalloenzyme drug development. However, MBPs can still suffer from pharmacokinetic liabilities. Bioisostere replacement is an effective strategy utilized by medicinal chemists to navigate these issues during the drug development process. The quinoline pharmacophore and its bioisosteres, such as quinazoline, are important building blocks in the design of new therapeutics. More relevant to metalloenzyme inhibition, 8-hydroxyquinoline (8-HQ) and its derivatives can serve as MBPs for metalloenzyme inhibition. In this report, 8-HQ isosteres are designed and the coordination chemistry of the resulting metal-binding isosteres (MBIs) is explored using a bioinorganic model complex. In addition, the physicochemical properties and metalloenzyme inhibition activity of these MBIs were investigated to establish drug-like profiles. This report provides a new group of 8-HQ-derived MBIs that can serve as novel scaffolds for metalloenzyme inhibitor development with tunable, and potentially improved, physicochemical properties.

Novel 5-fluorouracil complexes of Zn(II) with pyridine-based ligands as potential anticancer agents

A series of novel Zn(II) complexes of 5-fluorouracilate (5-FU), namely [Zn(5-FU)₂(bpy)] (1), [Zn(5-FU)₂(phen)] (2), [Zn(5-FU)₂(dpya)]·H₂O (3), [Zn(5-FU)₂(bpyma)]·2H₂O (4) and [Zn(5-FU)₂(terpy)]·H₂O (5), were synthesized and structurally characterized by spectroscopic methods and X-ray crystallography. 5-FU was coordinated to Zn(II) via the deprotonated N3 site and also presented the N1 and N3 linkage isomerism in 4 and 5 due to its tautomerism. The antiproliferative activity of the complexes was studied against lung (A549), breast (MDA-MB-231), colon (HCT116) and prostate (DU145) cancer cell lines. Complexes 1, 4 and 5 except 2 and 3 showed potent growth inhibitory activity towards selected cancer cells. Remarkably, 4 was highly cytotoxic towards A549 and MDA-MB-231 cell lines, being more active than the clinical drugs cisplatin and 5-FU. In addition, 4 was not toxic to normal lung cells (BEAS-2B). The complex exhibited a significantly high affinity towards DNA as assessed by gel electrophoresis and DNA docking. The mechanistic studies of 4 in A549 cells indicated that the complex induced apoptotic cell death as evidenced via caspase 3/7 activity, Bcl2 inactivation, annexin V and DAPI/PI staining. 4 further elevated the levels of reactive oxygen species (ROS), depolarized mitochondria and enhanced the expression of γ-H2AX, thus contributing to its remarkable anticancer activity.

Hydration and Charge-Transfer Effects of Alkaline Earth Metal Ions Binding to a Carboxylate Anion, Phosphate Anion, and Guanine Nucleobase

To investigate the ability of alkaline earth metal ions to tune ion-mediated DNA adsorption, hydrated Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ ions bound to a carboxylate anion, phosphate anion, and guanine nucleobase were modeled using density functional theory (DFT) and a combined explicit and continuum solvent model. The large first solvation shell of Ba²⁺ requires a larger solute cavity defined by a solvent-accessible surface, which is used to model all hydrated ions. Alkaline earth metal ions bind indirectly or directly to each binding site. DFT binding energies decrease with increasing ion size, which is likely due to ion size and hydration structure, rather than quantum effects such as charge transfer. However, charge transfer explains weaker ion binding to guanine compared to phosphate or carboxylate. Overall, carboxylate and phosphate anions are expected to compete equally for hydrated Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ ions and larger alkaline earth metal ions may induce weaker ion-mediated adsorption. The ion size and hydration structure of alkaline earth metal ions may effectively tune ion-mediated adsorption processes, such as DNA adsorption to functionalized surfaces.

Coupling 6-chloro-3-methyluracil with copper: structural features, theoretical analysis, and biofunctional properties

As nucleobases in RNA and DNA, uracil and 5-methyluracil represent a recognized class of bioactive molecules and versatile ligands for coordination compounds with various biofunctional properties. In this study, 6-chloro-3-methyluracil (Hcmu) was used as an unexplored building block for the self-assembly generation of a new bioactive copper(II) complex, [Cu(cmu)₂(H₂O)₂]·4H₂O (1). This compound was isolated as a stable crystalline solid and fully characterized in solution and solid state by a variety of spectroscopic methods (UV-vis, EPR, fluorescence spectroscopy), cyclic voltammetry, X-ray diffraction, and DFT calculations. The structural, topological, H-bonding, and Hirshfeld surface features of 1 were also analyzed in detail. The compound 1 shows a distorted octahedral {CuN₂O₄} coordination environment with two trans cmu^- ligands adopting a bidentate N,O-coordination mode. The monocopper(II) molecular units participate in strong H-bonding interactions with water molecules of crystallization, leading to structural 0D → 3D extension into a 3D H-bonded network with a tfz-d topology. Molecular docking and ADME analysis as well as antibacterial and antioxidant activity studies were performed to assess the bioactivity of 1. In particular, this compound exhibits a prominent antibacterial effect against Gram negative (E. coli, P. aeruginosa) and positive (S. aureus, B. cereus) bacteria. The obtained copper(II) complex also represents the first structurally characterized coordination compound derived from 6-chloro-3-methyluracil, thus introducing this bioactive building block into a family of uracil metal complexes with notable biofunctional properties.

Synthesis of Conjugated Polymers via Transition Metal Catalysed C-H Bond Activation

Transition metal catalysed C-H bond activation chemistry has emerged as an exciting and promising approach in organic synthesis. This allows us to synthesize a wider range of functional molecules and conjugated polymers in a more convenient and more atom economical way. The formation of C-C bonds in the construction of pi-conjugated systems, particularly for conjugated polymers, has benefited much from the advances in C-H bond activation chemistry. Compared to conventional transition-metal catalysed cross-coupling polymerization such as Suzuki and Stille cross-coupling, pre-functionalization of aromatic monomers, such as halogenation, borylation and stannylation, is no longer required for direct arylation polymerization (DArP), which involve C-H/C-X cross-coupling, and oxidative direct arylation polymerization (Ox-DArP), which involves C-H/C-H cross-coupling protocols driven by the activation of monomers' C(sp² )-H bonds. Furthermore, poly(annulation) via C-H bond activation chemistry leads to the formation of unique pi-conjugated moieties as part of the polymeric backbone. This review thus summarises advances to date in the synthesis of conjugated polymers utilizing transition metal catalysed C-H bond activation chemistry. A variety of conjugated polymers via DArP including poly(thiophene), thieno[3,4-c]pyrrole-4,6-dione)-containing, fluorenyl-containing, benzothiadiazole-containing and diketopyrrolopyrrole-containing copolymers, were summarized. Conjugated polymers obtained through Ox-DArP were outlined and compared. Furthermore, poly(annulation) using transition metal catalysed C-H bond activation chemistry was also reviewed. In the last part of this review, difficulties and perspective to make use of transition metal catalysed C-H activation polymerization to prepare conjugated polymers were discussed and commented.

Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications

Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.

A non-perturbative pairwise-additive analysis of charge transfer contributions to intermolecular interaction energies

A non-perturbative scheme for complete decomposition of energy and charge associated with charge transfer interaction into pairwise additive components.

DNA Binding and DNA Cleavage Activities of Newly Synthesized CoII and CuII Complexes of a β-Cyclodextrin Based Azo-Functionalized Schiff Base

Two water soluble complexes with CoII and CuII ions were synthesized using a novel β-cyclodextrin based azo-functionalized Schiff base as a ligand. The Schiff base and its metal complexes were characterized by different physico-chemical and spectroscopic methods. From the analyses of the experimental data, distorted octahedral geometry has been assigned for both the metal complexes. The binding interactions between the metal complexes and DNA were investigated by means of a thermal denaturation study and viscosity measurements as well as by electronic absorption and fluorescence spectroscopy. The DNA cleavage efficacy of the metal complexes was also studied by agarose gel electrophoresis using pBR DNA. These studies revealed that both the metal complexes followed an intercalative mode of binding to calf thymus (CT)-DNA and also effectively cleaved the supercoiled pBR DNA. The CoII complex, however, more efficiently cleaved CT-DNA than the CuII complex as much as the experimental results are concerned.

A theoretical study on the role of stability of cytosine and its tautomers in DNA (deoxyribonucleic acid), and investigation of interactions of Na+, K+, Mg2+, Ca2+, Zn2+ metal ions and OH radical with cytosine tautomers

In the present study, 21 cytosine tautomers were investigated so that some tautomers were reported for the first time in the gas phase and aqueous solution. C₃ tautomer was the most stable tautomer in gas phase but C₁ was the most stable structure in aqueous solution. The potential energy surface of all trajectories was determined for 21 tautomers and 22 transition states. Also, interactions of cytosine tautomers with Na⁺, K⁺, Mg²⁺, Ca²⁺ and Zn²⁺ metal ions were studied in gas phase and aqueous solution. Three types of interactions among metal ions and (N1 and O10), (N3 and O10) and (N3 and N9) of cytosine tautomers were investigated. The study of interaction energies of all complexes showed the stability of complexes in which interactions among Mg²⁺ and Zn²⁺ with tautomers were stronger than interactions among Ca²⁺, Na⁺ and K⁺ with tautomers, respectively. Some interactions of metal ions with cytosine tautomers made the most stable tautomers. So, the stability of rare tutomeric forms had a significant effect on stabilization of anomalous DNA (deoxyribonucleic acid) double helix and spontaneous mutations. Also, one of the most important causes of mutations in DNA (deoxyribonucleic acid) was the reaction of OH radical with nucleotide bases. So, interactions of OH radical with cytosine and its tautomers were investigated in gas phase and aqueous solution.Communicated by Ramaswamy H. Sarma.

The role of metal ion binding in the antioxidant mechanisms of reduced and oxidized glutathione in metal-mediated oxidative DNA damage

The antioxidant activity of glutathione in its reduced (GSH) and oxidized (GSSG) forms against metal-mediated oxidative DNA damage was studied by monitoring production of 8-hydroxy-2'-deoxyguanosine (8-OH-dG) from calf-thymus DNA. GSH and GSSG were combined with Fe(ii) and Cu(ii) before and after addition of DNA to investigate the role of metal coordination in the antioxidant mechanism. The antioxidant behavior of GSH and GSSG was also compared to the known radical scavenger DMSO. GSH and GSSG lower oxidative DNA damage for Fe(ii) and Cu(ii) reactions. GSH only exhibited appreciable antioxidant behavior when combined with Fe(ii) prior to adding DNA, and GSH and GSSG were slightly more effective against Cu(ii)-mediated damage when combined with Cu(ii) prior to adding DNA. Raman spectra of GSH in the presence of Cu(ii) indicate that Cu(ii) oxidizes GSH and raises the possibility that the antioxidant activity of GSH against Cu(ii) reactions may be attributed to its ability to form GSSG. No evidence of GSH oxidation in the presence of Fe(ii) was observed. The fluorescent probe dichlorofluorescein diacetate (DCF-DA) shows that the presence of GSH (for Cu(ii) reactions) and GSSG (for Fe(ii) and Cu(ii) reactions) lowers levels of reactive oxygen species (ROS) in bulk solution. Overall, the results suggest that the mechanism of antioxidant activity for GSH and GSSG against Fe(ii) and Cu(ii)-mediated oxidative damage involves metal coordination, and isothermal titration calorimetry (ITC) studies of the Cu(ii)-GSSG system show an enthalpically favored complexation reaction with an apparent 1 : 1 stoichiometry.

Contributions and competition of Mg2+ and K+ in folding and stabilization of the Twister ribozyme

Native folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg²⁺ in a background of monovalent ions. In a recent study, we have shown how the presence of Mg²⁺ impacts the transition from partially unfolded to folded states through a "push-pull" mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions. To further understand the ion atmosphere of RNA in folded and partially folded states results from atomistic umbrella sampling and oscillating chemical potential grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg²⁺ and K⁺ ions around Twister RNA. Results show the presence of 100 mM Mg²⁺ to lead to increased charge neutralization over that predicted by counterion condensation theory. Upon going from partially unfolded to folded states, overall charge neutralization increases at all studied ion concentrations that, while associated with an increase in the number of direct ion-phosphate interactions, is fully accounted for by the monovalent K⁺ ions. Furthermore, K⁺ preferentially interacts with purine N7 atoms of helical regions in partially unfolded states, thereby potentially stabilizing the helical regions. Thus, both secondary helical structures and formation of tertiary structures leads to increased counterion condensation, thereby stabilizing those structural features of Twister. Notably, it is shown that K⁺ can act as a surrogate for Mg²⁺ by participating in specific interactions with nonsequential phosphate pairs that occur in the folded state, explaining the ability of Twister to self-cleave at submillimolar Mg²⁺ concentrations.

Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson-Crick Edge

DNA duplexes comprising 6‐(1H‐pyrazol‐1‐yl)‐9H‐purine (6PP), 1‐deaza‐6PP (^1D6PP), 7‐deaza‐6PP (^7D6PP) and 1,7‐dideaza‐6PP (^1,7D6PP) 2′‐deoxyribonucleosides, respectively, were investigated towards their ability to form metal‐mediated base pairs in the presence of Ag^I. In 6PP and ^7D6PP, the Ag^I ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in ^1D6PP and ^1,7D6PP, so that in ^1D6PP an Ag^I coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the Ag^I‐binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of Ag^I, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1‐ or N7‐coordination is preferred in purine‐based metal‐mediated base pairs.

Stronger Cytotoxicity for Cancer Cells Than for Fast Proliferating Human Stem Cells by Rationally Designed Dinuclear Complexes

Cytostatic metallo-drugs mostly bind to the nucleobases of DNA. A new family of dinuclear transition metal complexes was rationally designed to selectively target the phosphate diesters of the DNA backbone by covalent bonding. The synthesis and characterization of the first dinuclear Ni^II₂ complex of this family are presented, and its DNA binding and interference with DNA synthesis in polymerase chain reaction (PCR) are investigated and compared to those of the analogous Cu^II₂ complex. The Ni^II₂ complex also binds to DNA but forms fewer intermolecular DNA cross-links, while it interferes with DNA synthesis in PCR at lower concentrations than Cu^II₂. To simulate possible competing phosphate-based ligands in vivo, these effects have been studied for both complexes with 100-200-fold excesses of phosphate and ATP, which provided no disturbance. The cytotoxicity of both complexes has been studied for human cancer cells and human stem cells with similar rates of proliferation. Cu^II₂ shows the lowest IC₅₀ values and a remarkable preference for killing the cancer cells. Three different assays show that the Cu^II₂ complex induces apoptosis in cancer cells. These results are discussed to gain insight into the mechanisms of action and demonstrate the potential of this family of dinuclear complexes as anticancer drugs acting by a new binding target.

Transition Metal Complexes with Flufenamic Acid for Pharmaceutical Applications-A Novel Three-Centered Coordination Polymer of Mn(II) Flufenamate

Five complexes of Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) with non-steroidal anti-inflammatory drug, flufenamic acid were synthesized: (1) [Mn₃(fluf)₆EtOH)(H₂O)]_·3EtOH; (2) [Co(fluf)₂(EtOH)(H₂O)]_·H₂O; (3) [Ni(fluf)₂(EtOH)(H₂O)]_·H₂O; (4) [Cu(fluf)_2·H₂O]; (5) [Zn(fluf)_2·H₂O]. All complexes were characterized by elemental analysis (EA), flame atomic absorption spectrometry (FAAS), Fourier-transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA). The crystal structure of 1 was determined by the single crystal X-ray diffraction technique. It crystallizes in the triclinic space group P with three independent Mn(II) cations, six coordinated flufenamato ligands augmented with water and ethanol molecules in the inner coordination sphere. In this crystal, manganese atoms are multiplied by symmetry and form infinite, polymeric chains which extend along the [001] dimension. The Hirshfeld Surface analysis revealed changes in interaction assemblies around all metal centers. The antioxidant and antimicrobial activities were established for all complexes and free ligand for comparison. All compounds exhibit good or moderate bioactivity against Gram-positive bacteria and yeasts.

Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity

Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications.

Chemosensing of Guanosine Triphosphate Based on a Fluorescent Dinuclear Zn(II)-Dipicolylamine Complex in Water

Guanosine triphosphate (GTP) is a key biomarker of multiple cellular processes and human diseases. The new fluorescent dinuclear complex [Zn₂(L)(S)][OTf]₄, 1 (asymmetric ligand, L = 5,8-Bis{[bis(2-pyridylmethyl)amino] methyl}quinoline, S = solvent, and OTf = triflate anion) was synthesized and studied in-depth as a chemosensor for nucleoside polyphosphates and inorganic anions in pure water. Additions at neutral pH of nucleoside triphosphates, guanosine diphosphate, guanosine monophosphate, and pyrophosphate (PPi) to 1 quench its blue emission (λ_em = 410 nm) with a pronounced selectivity toward GTP over other anions, including adenosine triphosphate (ATP), uridine triphosphate (UTP), and cytidine triphosphate (CTP). The efficient quenching response by the addition of GTP was observed in the presence of coexisting species in blood plasma and urine with a detection limit of 9.2 μmol L^-1. GTP also shows much tighter binding to the receptor 1 on a submicromolar level. On the basis of multiple spectroscopic tools (¹H, ³¹P NMR, UV-vis, and fluorescence) and DFT calculations, the binding mode is proposed through three-point recognition involving the simultaneous coordination of the N⁷ atom of the guanosine motif and two phosphate groups to the two Zn(II) atoms. Spectroscopic studies, MS-ESI, and DFT suggested that GTP bound to 1 in 1:1 and 2:2 models with high overall binding constants of log β_1 (1:1) = 6.05 ± 0.01 and log β₂ = 10.91 ± 0.03, respectively. The optical change and selectivity are attributed to the efficient binding of GTP to 1 by the combination of a strong electrostatic contribution and synergic effects of coordination bonds. Such GTP selectivity of an asymmetric metal-based receptor in water is still rare.

Anion–Cation Recognition Pattern, Thermal Stability and DFT-Calculations in the Crystal Structure of H2dap[Cd(HEDTA)(H2O)] Salt (H2dap = H2(N3,N7)-2,6-Diaminopurinium Cation)

The proton transfer between equimolar amounts of [Cd(H2EDTA)(H2O)] and 2,6-diaminopurine (Hdap) yielded crystals of the out-of-sphere metal complex H2(N3,N7)dap[Cd(HEDTA)(H2O)]·H2O (1) that was studied by single-crystal X-ray diffraction, thermogravimetry, FT-IR spectroscopy, density functional theory (DFT) and quantum theory of “atoms-in-molecules” (QTAIM) methods. The crystal was mainly dominated by H-bonds, favored by the observed tautomer of the 2,6-diaminopurinium(1+) cation. Each chelate anion was H-bonded to three neighboring cations; two of them were also connected by a symmetry-related anti-parallel π,π-staking interaction. Our results are in clear contrast with that previously reported for H2(N1,N9)ade [Cu(HEDTA)(H2O)]·2H2O (EGOWIG in Cambridge Structural Database (CSD), Hade = adenine), in which H-bonds and π,π-stacking played relevant roles in the anion–cation interaction and the recognition between two pairs of ions, respectively. Factors contributing in such remarkable differences are discussed on the basis of the additional presence of the exocyclic 2-amino group in 2,6-diaminopurinium(1+) ion.

DNA interaction, in vivo and in vitro cytotoxicity, reactive oxygen species, lipid peroxidation of -N, S donor Re(I) metal complexes

N, S donor ligands (L¹-L⁵){L¹-L⁵ = 1,5-bis(4-chlorophenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole (L¹), 1-(4-bromophenyl)-5-(4-chlorophenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole (L²), 5-(4-chlorophenyl)-3-(thiophen-2-yl)-1-(p-tolyl)-4,5-dihydro-1H-pyrazole (L³), 5-(4-chlorophenyl)-1-(4-methoxyphenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole (L⁴), 5-(4-chlorophenyl)-1-(4-nitrophenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole (L⁵)} were synthesized by Claisen-Schmidt condensation and characterized by spectrometric methods. The complexes (I-V) were synthesized by ligand combination followed by metal chelation. The binding of the rhenium complexes to Herrin sperm DNA was monitored by UV spectroscopy and viscosity measurements. The groove binding was suggested as the most possible mode, and the K_b values of the complexes were calculated. The mode of interaction was furthermore confirmed by molecular docking. Brine shrimp lethality and Saccharomyces cerevisiae cytotoxicity against the eukaryotic and prokaryotic cells showed the toxic nature of the synthesized compounds. All compounds were found active against S. cerevisiae, which was confirmed by increased ROS production, and DNA damage as compared to untreated yeast cell culture. The oxidative harm to cell structures was affirmed by lipid peroxidation. An antimicrobial study was carried out by estimating minimum inhibitory concentration against two Gram-positive and three Gram-negative bacteria. All complexes show good antiproliferative activity against the HCT 116 cell line. All synthesized complexes are biologically more active than the corresponding ligands.