Development of a multi-targeted chemotherapeutic approach based on G-quadruplex stabilisation and carbonic anhydrase inhibition.

A novel class of compounds designed to hit two anti-tumour targets, G-quadruplex structures and human carbonic anhydrases (hCAs) IX and XII is proposed. The induction/stabilisation of G-quadruplex structures by small molecules has emerged as an anticancer strategy, disrupting telomere maintenance and reducing oncogene expression. hCAs IX and XII are well-established anti-tumour targets, upregulated in many hypoxic tumours and contributing to metastasis. The ligands reported feature a berberine G-quadruplex stabiliser scaffold connected to a moiety inhibiting hCAs IX and XII. In vitro experiments showed that our compounds selectively stabilise G-quadruplex structures and inhibit hCAs IX and XII. The crystal structure of a telomeric G-quadruplex in complex with one of these ligands was obtained, shedding light on the ligand/target interaction mode. The most promising ligands showed significant cytotoxicity against CA IX-positive HeLa cancer cells in hypoxia, and the ability to stabilise G-quadruplexes within tumour cells.

Old Acquaintances and Novel Complex Structures for the Ni(II) and Cu(II) Complexes of bis-Chelate Oxime-Amide Ligands.

In the process of systematically studying the methylhydroxyiminoethaneamide bis-chelate ligands with polymethylene spacers of different lengths, L1-L3, and their transition metal complexes, a number of new Ni(II) and Cu(II) species have been isolated, and their molecular and crystal structures were determined using single-crystal X-ray diffraction. In all of these compounds, the divalent metal is coordinated by the ligand donor atoms in a square-planar arrangement. In addition, a serendipitously discovered new type of neutral Ni(II) complex, where the propane spacer of ligand L2 underwent oxidation to the propene spacer, and one of the amide groups was oxidised to the ketoimine, is also reported. The resulting ligand L2' affords the formation of neutral planar Ni(II) complexes, which are assembled in the solid state on top of each other, and yield two polymorphic structures. In both structures, the resulting infinite, exclusively parallel metal ion columns in ligand insulation may serve as precursor materials for sub-nano-conducting connectors. Overall, this paper reports the synthesis and characterisation of seven new anionic, cationic, and neutral Ni(II) and Cu(II) complexes, their crystal structures, as well as experimental and computed UV-Vis absorption spectra for two structurally similar Ni(II) complexes, yellow and red.

A Norbornadiene-Based Molecular System for the Storage of Solar-Thermal Energy in an Aqueous Solution: Study of the Heat-Release Process Triggered by a Co(II)-Complex.

It is urgent yet challenging to develop new environmentally friendly and cost-effective sources of energy. Molecular solar thermal (MOST) systems for energy capture and storage are a promising option. With this in mind, we have prepared a new water-soluble (pH > 6) norbornadiene derivative (HNBD1) whose MOST properties are reported here. HNBD1 shows a better matching to the solar spectrum compared to unmodified norbornadiene, with an onset absorbance of λonset = 364 nm. The corresponding quadricyclane photoisomer (HQC1) is quantitatively generated through the light irradiation of HNBD1. In an alkaline aqueous solution, the MOST system consists of the NBD1-/QC1- pair of deprotonated species. QC1- is very stable toward thermal back-conversion to NBD1-; it is absolutely stable at 298 K for three months and shows a marked resistance to temperature increase (half-life t½ = 587 h at 371 K). Yet, it rapidly (t½ = 11 min) releases the stored energy in the presence of the Co(II) porphyrin catalyst Co-TPPC (ΔHstorage = 65(2) kJ∙mol-1). Under the explored conditions, Co-TPPC maintains its catalytic activity for at least 200 turnovers. These results are very promising for the creation of MOST systems that work in water, a very interesting solvent for environmental sustainability, and offer a strong incentive to continue research towards this goal.

Assembly of Polyiodide Networks with Cu(II) Complexes of Pyridinol-Based Tetraaza Macrocycles.

Polyiodide networks are currently of great practical interest for the preparation of new electronic materials. The participation of metals in the formation of these networks is believed to improve their mechanical performance and thermal stability. Here we report the results on the construction of polyiodide networks obtained using Cu(II) complexes of a series of pyridinol-based tetraazacyclophanes as countercations. The assembly of these crystalline polyiodides takes place from aqueous solutions on the basis of similar structural elements, the [CuL]2+ and [Cu(H-1L)]+ (L = L2, L2-Me, L2-Me3) complex cations, so that the peculiarities induced by the increase of N-methylation of ligands, the structural variable of ligands, can be highlighted. First, solution equilibria involving ligands and complexes were analyzed (potentiometry, NMR, UV-vis, ITC). Then, the appropriate conditions could be selected to prepare polyiodides based on the above complex cations. Single-crystal XRD analysis showed that the coordination of pyridinol units to two metal ions is a prime feature of these ligands, leading to polymeric coordination chains of general formula {[Cu(H-1L)]}nn+ (L = L2-Me, L2-Me3). In the presence of the I-/I2 couple, the polymerization tendency stops with the formation of [(CuL)(CuH-1L)]3+ (L = L2-Me, L2-Me3) dimers which are surrounded by polyiodide networks. Moreover, coordination of the pyridinol group to two metal ions transforms the surface charge of the ring from negative to markedly positive, generating a suitable environment for the assembly of polyiodide anions, while N-methylation shifts the directional control of the assembly from H-bonds to I···I interactions. In fact, an extended concatenation of iodine atoms occurs around the complex dimeric cations, the supramolecular I···I interactions become shorter and shorter, fading into stronger forces dominated by the orbital overlap, which is promising for effective electronic materials.

Noncovalent Assembly and Catalytic Activity of Hybrid Materials Based on Pd Complexes Adsorbed on Multiwalled Carbon Nanotubes, Graphene, and Graphene Nanoplatelets.

Green catalysts with excellent performance in Cu-free Sonogashira coupling reactions can be prepared by the supramolecular decoration of graphene surfaces with Pd(II) complexes. Here we report the synthesis, characterization, and catalytic properties of new catalysts obtained by the surface decoration of multiwalled carbon nanotubes (MWCNTs), graphene (G), and graphene nanoplatelets (GNPTs) with Pd(II) complexes of tetraaza-macrocyclic ligands bearing one or two anchor functionalities. The decoration of these carbon surfaces takes place under environmentally friendly conditions (water, room temperature, aerobic) in two steps: (i) π-π stacking attachment of the ligand via electron-poor anchor group 6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxo-pyrimidine and (ii) Pd(II) coordination from PdCl42-. Ligands are more efficiently adsorbed on the flat surfaces of G and GNPTs than on the curved surfaces of MWCNTs. All catalysts work very efficiently under mild conditions (50 °C, aerobic, 7 h), giving a similar high yield (90% or greater) in the coupling of iodobenzene with phenylacetylene to form diphenylacetylene in one catalytic cycle, but catalysts based on G and GNPTs (especially on GNPTs) provide greater catalytic efficiency in reuse (four cycles). The study also revealed that the active centers of the ligand-Pd type decorating the support surfaces are much more efficient than the Pd(0) and PdCl42- centers sharing the same surfaces. All of the results allow a better understanding of the structural factors to be controlled in order to obtain an optimal efficiency from similar catalysts based on graphene supports.

Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis.

The interaction between the series of berberine derivatives 1-5 (NAX071, NAX120, NAX075, NAX077 and NAX079) and human telomeric G-quadruplexes (G4), which are able to inhibit the Telomerase enzyme's activity in malignant cells, was investigated. The derivatives bear a pyridine moiety connected by a hydrocarbon linker of varying length (n = 1-5, with n number of aliphatic carbon atoms) to the C13 position of the parent berberine. As for the G4s, both bimolecular 5'-TAGGGTTAGGGT-3' (Tel12) and monomolecular 5'-TAGGGTTAGGGTTAGGGTTAGGG-3' (Tel23) DNA oligonucleotides were considered. Spectrophotometric titrations, melting tests, X-ray diffraction solid state analysis and in silico molecular dynamics (MD) simulations were used to describe the different systems. The results were compared in search of structure-activity relationships. The analysis pointed out the formation of 1:1 complexes between Tel12 and all ligands, whereas both 1:1 and 2:1 ligand/G4 stoichiometries were found for the adduct formed by NAX071 (n = 1). Tel12, with tetrads free from the hindrance by the loop, showed a higher affinity. The details of the different binding geometries were discussed, highlighting the importance of H-bonds given by the berberine benzodioxole group and a correlation between the strength of binding and the hydrocarbon linker length. Theoretical (MD) and experimental (X-ray) structural studies evidence the possibility for the berberine core to interact with one or both G4 strands, depending on the constraints given by the linker length, thus affecting the G4 stabilization effect.

Porous Frameworks Based on Supramolecular Ball Joints: Bringing Flexibility to Ordered 3D Lattices.

XOFs-type materials (X=M, C, S, that is, metal-organic frameworks, covalent organic frameworks and supramolecular organic frameworks, respectively) share a common unifying feature: mutual spatial orientation of constituting components is strictly directional and unchanging by design. Herein, we illustrate an alternate design for porous architectures, as rigid joints constituted by coordinative (MOFs), covalent (COFs), or hydrogen-donor/acceptor (SOFs) bonds, are replaced by supramolecular ball joints, which confer unprecedented flexibility, especially angular, to porous networks. The obtained frameworks remain highly organized but are also permutable: lacking a forced convergence towards an immutable minimum energy structure, these systems remain able to adjust depending on external conditions. Results of POF (permutable organized framework) synthesis is a family of structures rather than a single pre-determined three-dimensional arrangement, as we demonstrate with an illustrative set of 5 XRD structures.

Stabilisation of Exotic Tribromide (Br3-) Anions via Supramolecular Interaction with A Tosylated Macrocyclic Pyridinophane. A Serendipitous Case.

Tetraaza-macrocyclic pyridinophane L-Ts, decorated with a p-toluenesulfonyl (tosyl; Ts) group, appear to be a useful tool to provide evidence on how the interplay of various supramolecular forces can help stabilise exotic anionic species such as tribromide (Br3-) anions. Indeed, crystals of (H2L-Ts)(Br3)1.5(NO3)0.5 unexpectedly grew from an acidic (HNO3) aqueous solution of L-Ts in the presence of Br- anions. The crystal structure of this compound was determined by single crystal XRD analysis. Hydrogen bonds, salt-bridges, anion-, - stacking, and van der Waals interactions contribute to stabilising the crystal lattice. The observation of two independent Br3- anions stuck over the π-electron densities of pyridine and tosyl ligand groups, one of them being sandwiched between two pyridine rings, corroborates the significance of anion-π interactions for N-containing heterocycles. We show herein the possibility of detecting anion-π contacts from fingerprint plots generated by Hirshfeld surface analysis, demonstrating the effective usage of this structural investigation technique to further dissect individual contributions of stabilising supramolecular forces.

Sensing Zn2+ in Aqueous Solution with a Fluorescent Scorpiand Macrocyclic Ligand Decorated with an Anthracene Bearing Tail.

Synthesis of the new scorpiand ligand L composed of a [9]aneN3 macrocyclic ring bearing a CH2CH2NHCH2-anthracene tail is reported. L forms both cation (Zn2+) and anion (phosphate, benzoate) complexes. In addition, the zinc complexes of L bind these anions. The equilibrium constants for ligand protonation and complex formation were determined in 0.1 M NaCl aqueous solution at 298.1 ± 0.1 K by means of potentiometric (pH-metric) titrations. pH Controlled coordination/detachment of the ligand tail to Zn2+ switch on and off the fluorescence emission from the anthracene fluorophore. Accordingly, L is able to sense Zn2+ in the pH range 6-10 down to nM concentrations of the metal ion. L can efficiently sense Zn2+ even in the presence of large excess of coordinating anions, such as cyanide, sulphide, phosphate and benzoate, despite their ability to bind the metal ion.

Effect of structure levels on surface-enhanced Raman scattering of human telomeric G-quadruplexes in diluted and crowded media.

Human telomeric G-quadruplexes are emerging targets in anticancer drug discovery since they are able to efficiently inhibit telomerase, an enzyme which is greatly involved in telomere instability and immortalization process in malignant cells. G-quadruplex (G4) DNA is highly polymorphic and can adopt different topologies upon addition of electrolytes, additives, and ligands. The study of G-quadruplex forms under various conditions, however, might be quite challenging. In this work, surface-enhanced Raman scattering (SERS) spectroscopy has been applied to study G-quadruplexes formed by human telomeric sequences, d[A3G3(TTAGGG)3A2] (Tel26) and d[(TTAGGG)4T2] (wtTel26), under dilute and crowding conditions. The SERS spectra distinctive of hybrid-1 and hybrid-2 G-quadruplexes of Tel26 and wtTel26, respectively, were observed for the sequences folded in the presence of K+ ions (110 mM) in a buffered solution, representing the diluted medium. Polyethylene glycol (5, 10, 15, 20, and 40% v/v PEG) was used to create a molecular-crowded environment, resulting in the formation of the parallel G-quadruplexes of both studied human telomeric sequences. Despite extensive overlap by the crowding agent bands, the SERS spectral features indicative of parallel G4 form of Tel26 were recognized. The obtained results implied that SERS of G-quadruplexes reflected not only the primary structure of the studied human telomeric sequence, including its nucleobase composition and sequence, but also its secondary structure in the sense of Hoogsteen hydrogen bonds responsible for the guanine tetrad formation, and finally its tertiary structure, defining a three-dimensional DNA shape, positioned close to the enhancing metallic surface. Graphical abstract.

Tales of the Unexpected: The Case of Zirconium(IV) Complexes with Desferrioxamine.

The Zr4+ complexes with desferrioxamine (H3DFO) and its derivatives are the only 89Zr-based imaging agents for proton emission tomography (PET) that have been used so far in clinical trials. Nevertheless, a complete speciation of the Zr4+/H3DFO system in solution has never been performed and the stability constants of the relevant complexes are still unknown. Here we report, for the first time, the speciation of this system in water, performed by potentiometric titrations, and the determination of the stability constants of all complexes formed in the pH range 2.5-11.5. Surprisingly, although desferrioxamine gives rise to very stable 1:1 complexes with Zr4+ (logK = 36.14 for Zr4+ + DFO3- = [ZrDFO]+), 2:2 and 2:3 ones are also formed in solution. Depending on the conditions, these binuclear complexes can be main species in solution. These results were corroborated by small-angle X-ray scattering (SAXS) and MALDI mass spectrometry analyses of complex solutions. Information on complex structures was obtained by means of density functional theory (DFT) calculations.

Solid State and Solution Study on the Formation of Inorganic Anion Complexes with a Series of Tetrazine-Based Ligands.

Four molecules (L1-L4) constituted by an s-tetrazine ring appended with two identical aliphatic chains of increasing length bearing terminal morpholine groups were studied as anion receptors in water. The basicity properties of these molecules were also investigated. Speciation of the anion complexes formed in solution and determination of their stability constants were performed by means of potentiometric (pH-metric) titrations, while further information was obtained by NMR and isothermal titration calorimetry (ITC) measurements. The crystal structures of two neutral ligands (L3, L4) and of their H2L3(ClO4)2∙2H2O, H2L4(ClO4)2∙2H2O, H2L3(PF6)2, and H2L3(PF6)2∙2H2O anion complexes were determined by single crystal X-ray diffraction. The formation of anion-π interactions is the leitmotiv of these complexes, both in solution and in the solid state, although hydrogen bonding and/or formation of salt-bridges can contribute to their stability. Evidence of the ability of these ligands to form anion-π interactions is given by the observation that even the neutral (not-protonated) molecules bind anions in water to form complexes of significant stability, including elusive OH- anions.

Induction of a Four-Way Junction Structure in the DNA Palindromic Hexanucleotide 5'-d(CGTACG)-3' by a Mononuclear Platinum Complex.

Four-way junctions (4WJs) are supramolecular DNA assemblies comprising four interacting DNA strands that in biology are involved in DNA-damage repair. In this study, a new mononuclear platinum(II) complex 1 was prepared that is capable of driving the crystallization of the DNA oligomer 5'-d(CGTACG)-3' specifically into a 4WJ-like motif. In the crystal structure of the 1-CGTACG adduct, the distorted-square-planar platinum complex binds to the core of the 4WJ-like motif through π-π stacking and hydrogen bonding, without forming any platinum-nitrogen coordination bonds. Our observations suggest that the specific molecular properties of the metal complex are crucially responsible for triggering the selective assembly of this peculiar DNA superstructure.

Deciphering the Mechanism of Human Carbonic Anhydrases Inhibition with Sulfocoumarins: Computational and Experimental Studies.

The reaction mechanism of the carbonic anhydrase-mediated hydrolysis of sulfocoumarins to sulfonic acids has been investigated on an enzyme cluster model using the B3LYP hybrid density functional theory (DFT) and the QST procedure for the Transition State (TS) search. A multistep process was highlighted, with the rate-determining step identified in the initial dual nucleophilic/acidic attack of the zinc-bound hydroxide ion to the sulfocoumarin sulfur atom and to the C3=C4 double bond. The reported multi-step process, combined to SAR analysis on a new set of derivatives, highlighted unprecedented mechanistic aspects of the CA-mediated prodrug activation, which in turn possess relevant consequences to the isoforms-selective inhibition profiles reported by such a class of compounds.

Network Formation via Anion Coordination: Crystal Structures Based on the Interplay of Non-Covalent Interactions.

We describe the synthesis and the structural characterization of new H2L(CF3CO2)2 (1) and H2L(Ph2PO4)2 (2) compounds containing the diprotonated form (H2L2+) of the tetrazine-based molecule 3,6-di(pyridin-4-yl)-1,2,4,5-tetrazine. X-ray diffraction (XRD) analysis of single crystals of these compounds showed that H2L2+ displays similar binding properties toward both anions when salt bridge interactions are taken into account. Nevertheless, the different shapes, sizes and functionalities of trifluoroacetate and diphenyl phosphate anions define quite different organization patterns leading to the peculiar crystal lattices of 1 and 2. These three-dimensional (3D) architectures are self-assembled by a variety of non-covalent forces, among which prominent roles are played by fluorine-π (in 1) and anion-π (in 2) interactions.

[Au(9-methylcaffein-8-ylidene)2 ]+ /DNA Tel23 System: Solution, Computational, and Biological Studies.

Physicochemical methods have been used to investigate interactions occurring in solution between the dicarbene gold(I) complex [Au(9-methylcaffein-8-ylidene)2 ]BF4 (AuNHC) and a human telomeric DNA sequence, namely Tel23. Circular dichroism measurements allow identification of the conformational changes experienced by Tel23 upon interaction with AuNHC, and the respective binding stoichiometries and constants were determined. Computational studies provide a good link between previous crystallographic results of the same system and the present solution data, offering an exhaustive description of the inherent noncovalent metallodrug-DNA interactions. Remarkably, we found that a preformed AuNHC/Tel23 adduct is capable of producing strong and selective inhibition of the enzyme telomerase. The latter feature is mechanistically relevant and might account for the conspicuous in vitro anticancer properties of the investigated dicarbene gold(I) complex.

Assessment of human telomeric G-quadruplex structures using surface-enhanced Raman spectroscopy.

G-Quadruplex (G4) structures of a human telomeric 24-mer (5'-TTAGGGTTAGGGTTAGGGTTAGGG-3') sequence (Tel24) stabilized by sodium and potassium ions have been assessed using surface-enhanced Raman scattering (SERS) spectroscopy. The distinctive SERS spectra of Tel24 in the presence of 100 mM Na+ and 100 mM K+ were obtained and the SERS bands characteristic of the antiparallel basket-type and the mixed hybrid (3+1) structures, respectively, were identified and assigned. The influence of the SERS - active substrate on the scattering enhancement was studied using citrate- and chloride-covered silver nanoparticles, in the absence and presence of the aggregating agent (0.1 M Na2SO4 and 0.1 M K2SO4). The highly reproducible SERS spectra of Tel24 obtained in various SERS active media indicated the same adsorption mechanism of the cation - stabilized G-quadruplexes onto the metal surface, regardless of the silver colloid. The remarkable resemblance between the circular dichroism (CD) spectra of the Tel24 structures with and without the colloid confirmed that interaction with the enhancing silver surface did not affect the stability of the formed G4 structures. The presented study pointed to a great potential of the SERS spectroscopy for the sensitive structural analysis of various G4 topologies. Graphical Abstract SERS spectroscopy allowed identification of Na+ stabilized antiparallel basket-type and K+ stabilized hybrid (3+1) structures of the same 24-mer human telomeric sequence.

Cation, Anion and Ion-Pair Complexes with a G-3 Poly(ethylene imine) Dendrimer in Aqueous Solution.

The G-3 poly(ethylene imine) ligand L2 shows a multifaceted coordination ability, being able to bind metal cations, anions and ion-pairs. The equilibrium constants for the formation of metal (Cu2+, Zn2+), anion (SO42-) and ion-pair (Cu2+/SO42-) complexes were determined in 0.1 M Me4NCl aqueous solution at 298.1 ± 0.1 K by means of potentiometric titrations. Thanks to its dendrimeric nature, L2 can form highly nucleated metal complexes, such as Cu5L210+ and Zn4L28+, in successive and well-defined complexation steps. Protonated forms of L2 give rise to relatively weak anion complexes with SO42-, but the addition of Cu2+ significantly enhances the binding ability of the ligand toward this anion below pH 9. In more alkaline solutions, an opposite trend is observed. The coordination properties of L2 are discussed with the support of modelling calculations. According to results, L2 is a promising molecule for the preparation of solid supported materials for the recovery of cations and anions from aqueous media and/or for applications in heterogeneous catalysis.

Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding.

Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination.

Anion Complexes with Tetrazine-Based Ligands: Formation of Strong Anion-π Interactions in Solution and in the Solid State.

Ligands L1 and L2, consisting of a tetrazine ring decorated with two morpholine pendants of different lengths, show peculiar anion-binding behaviors. In several cases, even the neutral ligands, in addition to their protonated HL(+) and H2L(2+) (L = L1 and L2) forms, bind anions such as F(-), NO3(-), PF6(-), ClO4(-), and SO4(2-) to form stable complexes in water. The crystal structures of H2L1(PF6)2·2H2O, H2L1(ClO4)2·2H2O, H2L2(NO3)2, H2L2(PF6)2·H2O, and H2L2(ClO4)2·H2O show that anion-π interactions are pivotal for the formation of these complexes, although other weak forces may contribute to their stability. Complex stability constants were determined by means of potentiometric titration in aqueous solution at 298.1 K, while dissection of the free-energy change of association (ΔG°) into its enthalpic (ΔH°) and entropic (TΔS°) components was accomplished by means of isothermal titration calorimetry measurements. Stability constants are poorly regulated by anion-ligand charge-charge attraction. Thermodynamic data show that the formation of complexes with neutral ligands, which are principally stabilized by anion-π interactions, is enthalpically favorable (-ΔG°, 11.1-17.5 kJ/mol; ΔH°, -2.3 to -0.5 kJ/mol; TΔS°, 9.0-17.0 kJ/mol), while for charged ligands, enthalpy changes are mostly unfavorable. Complexation reactions are invariably promoted by large and favorable entropic contributions. The importance of desolvation phenomena manifested by such thermodynamic data was confirmed by the hydrodynamic results obtained by means of diffusion NMR spectroscopy. In the case of L2, complexation equilibria were also studied in a 80:20 (v/v) water/ethanol mixture. In this mixed solvent of lower dielectric constant than water, the stability of anion complexes decreases, relative to water. Solvation effects, mostly involving the ligand, are thought to be responsible for this peculiar behavior.