A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database

Knowledge about the 3-dimensional structure, orientation and interaction of chemical compounds is important in many areas of science and technology. X-ray crystallography is one of the experimental techniques capable of providing a large amount of structural information for a given compound, and it is widely used for characterisation of organic and metal-organic molecules. The method provides precise 3D coordinates of atoms inside crystals, however, it does not directly deliver information about certain chemical characteristics such as bond orders, delocalization, charges, lone electron pairs or lone electrons. These aspects of a molecular model have to be derived from crystallographic data using refined information about interatomic distances and atom types as well as employing general chemical knowledge. This publication describes a curated automatic pipeline for the derivation of chemical attributes of molecules from crystallographic models. The method is applied to build a catalogue of chemical entities in an open-access crystallographic database, the Crystallography Open Database (COD). The catalogue of such chemical entities is provided openly as a derived database. The content of this catalogue and the problems arising in the fully automated pipeline are discussed, along with the possibilities to introduce manual data curation into the process.

Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions

Published reports of chemical compounds often contain multiple machine-readable descriptions which may supplement each other in order to yield coherent and complete chemical representations. This publication presents a method to cross-check such descriptions using a canonical representation and isomorphism of molecular graphs. If immediate agreement between compound descriptions is not found, the algorithm derives the minimal set of simplifications required for both descriptions to arrive to a matching form (if any). The proposed algorithm is used to cross-check chemical descriptions from the Crystallography Open Database to identify coherently described entries as well as those requiring further curation.

Improvement of the Proton Conduction of Copper(II)-Mesoxalate Metal-Organic Frameworks by Strategic Selection of the Counterions

Three copper(II)/mesoxalate-based MOFs with formulas (H₃O)[Cu₉(Hmesox)₆(H₂O)₆Cl]·8H₂O (1), (NH₂Me₂)_0.4(H₃O)_0.6[Cu₉(Hmesox)₆(H₂O)₆Cl]·8H₂O (2), and (enH₂)_0.25(enH)_1.5[Cu₆(Hmesox)₃(mesox)(H₂O)₆Cl_0.5]Cl_0.5·5.25H₂O (3) were synthesized (H₄mesox = mesoxalic acid = 2,2-dihydroxypropanedioic acid, en = ethylenediamine). Essentially, all of the compounds display the same anionic network with a different arrangement of the cations, which have a remarkable effect on the proton conduction of the materials, ranging from 1.16 × 10^–4 S cm^–1 for 1 to 1.87 × 10^–3 S cm^–1 for 3 (at 80 °C and 95% RH). These compounds also display antiferromagnetic coupling among the copper(II) ions through both the carboxylate and alkoxido bridges. The values of the principal magnetic coupling constants were calculated by density functional theory (DFT), leading to congruent values that confirm the predominant antiferromagnetic nature of the interactions.

Three copper(II)-mesoxalate metal−organic frameworks were synthesized in the presence of three different cations: hydronium, dimethylammonium, and ethylenediammonium, which neutralize the charge of the anionic networks. Besides the crystallographic characterization and the investigation of the magnetic properties, the compounds show varying proton conductivities depending on the included cations. The proton conductivity increases 1 order of magnitude in the case of compound 3 (1.87 × 10⁻³ S cm⁻¹ at 80 °C and 95% RH), which contains ethylenediammonium cations.

Zinc 1,2,4-triazolo[1,5-a]pyrimidine complexes: synthesis, structural characterization and their effect against Chagas disease

BACKGROUND

The World Health Organization catalogues illnesses such as Chagas disease as neglected diseases, due the low investment in new drugs to fight them. The search for novel and non-side effects anti-parasitic compounds is one of the urgent needs of the Third World. The use of triazolopyrimidines and their metal complexes have demonstrated hopeful results in this field.

OBJECTIVE

This work studies the antiparasitic efficacy against Trypanosoma cruzi strains of a series of zinc triazolopyrimidine complexes.

METHOD

A series of Zn complexes has been synthesized by the reaction between the triazolopyrimidine derivatives 7-amino-1,2,4-triazolo[1,5-a]pyrimidine (7atp) and 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp) with Zn(SO4) • 7H2O, ZnCl2, and Zn(NO3)2 • 6H2O salts. The complexes have been analyzed by spectroscopic and thermal assays and X-ray diffraction methods have been used to dilucidate the crystalline structure of one of them. The antiparasitic efficacy was tested in vitro against Trypanosoma cruzi to compare the trypanocidal effect of different ligands and counteranions to fight Chagas disease.

RESULTS

The efficacy of these compounds against Trypanosoma cruzi has also been tested to compare the influence of different ligands and counteranions on the trypanocidal effect against Chagas disease.

CONCLUSION

Antiproliferative tests corroborate the synergistic trypanocidal effect of the triazolopyrimidine coordination complexes.

Anti-diabetic and anti-parasitic properties of a family of luminescent zinc coordination compounds based on the 7-amino-5-methyl-1,2,4-triazolo[1,5-a]pyrimidine ligand

We report on the formation of a triazolopyrimidine derivative ligand, 7-amino-5-methyl-1,2,4-triazolo[1,5-a]pyrimidine (7-amtp), and a new family of coordination compounds based on this ligand and zinc as metal ion, synthesized by conventional routes. These materials possess different mononuclear structures, namely [ZnCl₂(7-amtp)₂] (1), [Zn(7-amtp)₂(H₂O)₄](NO₃)₂·2(7-amtp)·6H₂O (2) and [Zn(7-amtp)₂(H₂O)₄](SO₄)·1.5H₂O (3) derived from the use of different zinc (II) salts, in such a way that the counterions govern the crystallization to a large extent. These compounds present and show variable luminescent properties based on ligand-centred charge transfers which have been deeply studied by Time Dependent Density Functional Theory (TD-DFT) calculations. When these compounds are transferred to solution, preserving complex entities as corroborated by NMR studies, they present interesting anti-diabetic and anti-parasitic capabilities, with a comparatively higher selectivity index than other previously reported triazolopyrimidine-based materials. The results derived from in vivo experiments conducted in mice also confirm their promising activity as anti-diabetic drug being capable of dropping glucose levels after oral administration. Therefore, these new materials may be considered as excellent candidates to be further investigated in the field of luminescent coordination compounds with biomedical applications.

IFN-γ-tethered hydrogels enhance mesenchymal stem cell-based immunomodulation and promote tissue repair

Because of their immunomodulatory activities, human mesenchymal stem cells (hMSCs) are being explored to treat a variety of chronic conditions such as inflammatory bowel disorders and graft-vs-host disease. Treating hMSCs with IFN-γ prior to administration augments these immunomodulatory properties; however, this ex vivo treatment limits the broad applicability of this therapy due to technical and regulatory issues. In this study, we engineered an injectable synthetic hydrogel with tethered recombinant IFN-γ that activates encapsulated hMSCs to increase their immunomodulatory functions and avoids the need for ex vivo manipulation. Tethering IFN-γ to the hydrogel increases retention of IFN-γ within the biomaterial while preserving its biological activity. hMSCs encapsulated within hydrogels with tethered IFN-γ exhibited significant differences in cytokine secretion and showed a potent ability to halt activated T-cell proliferation and monocyte-derived dendritic cell differentiation compared to hMSCs that were pre-treated with IFN-γ and untreated hMSCs. Importantly, hMSCs encapsulated within hydrogels with tethered IFN-γ accelerated healing of colonic mucosal wounds in both immunocompromised and immunocompetent mice. This novel approach for licensing hMSCs with IFN-γ may enhance the clinical translation and efficacy of hMSC-based therapies.

PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery

In vitro differentiation of human pluripotent stem cell (hPSC)-derived organoids (HOs) facilitates the production of multicellular three-dimensional structures analogous to native human tissues. Most current methods for the generation of HOs rely on Matrigel, a poorly defined basement membrane derivative secreted by Engelbreth-Holm-Swarm mouse sarcoma cells, limiting the potential use of HOs for regenerative medicine applications. Here, we describe a protocol for the synthesis of a fully defined, synthetic hydrogel that supports the generation and culture of HOs. Modular, cell-encapsulating hydrogels are formed from a four-armed poly(ethylene glycol) macromer that has maleimide groups at each terminus (PEG-4MAL) and is conjugated to cysteine-containing adhesive peptides and cross-linked via protease-degradable peptides. The protocol also includes guidelines for the localized in vivo delivery of PEG-4MAL hydrogel-encapsulated HOs to injured mouse colon. The PEG-4MAL hydrogel supports the engraftment of the HOs and accelerates colonic wound repair. This culture and delivery strategy can thus be used to develop HO-based therapies to treat injury and disease. Hydrogel and tissue preparation and subsequent encapsulation can be performed within 2.5-3.5 h. Once HOs have been cultured in synthetic hydrogels for at least 14 d, they can be prepared and delivered to the mouse colon in under 5 h.

First Example of Antiparasitic Activity Influenced by Thermochromism: Leishmanicidal Evaluation of 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine Metal Complexes

BACKGROUND

The World Health Organization catalogues illnesses such as Leishmaniasis as neglected diseases, due to low investment in new drugs to fight them. The search of novel and non-side effects anti-parasitic compounds is one of the urgent needs for the Third World. The use of triazolopyrimidines and their metallic complexes has demonstrated hopeful results in this field.

OBJECTIVE

This work studies the antiparasitic efficacy of a series of 5,7-dimethyl-1,2,4- triazolo[1,5-a]pyrimidine first row transition metal complexes against three leishmania spp. strains.

METHODS

The in vitro antiproliferation of promastigote forms of different strains of leishmania spp. (L. infantum, L. braziliensis and L donovani) and the cytotoxicity in macrophage host cells are reported here. The antiparasitic assays have been complemented with enzymatic tests to elucidate the mechanisms of action. New crystal structure description, thermal analysis, magnetic susceptibility and magnetization experiments have also been carried out in order to present a whole characterization of the studied compounds and interesting physical properties besides the biological tests.

RESULTS

The results of antiproliferation screening and cytotoxicity show great antiparasitic efficacy in the studied complexes. The superoxide dismutase enzymatic assays exhibit a different behaviour according to the thermochromic triazolopyrimidine form tested.

CONCLUSION

Antiproliferative assays and enzymatic tests corroborate the synergetic leishmanicidal effect present in coordination triazolopyrimidine complexes. The changes in coordination sphere derived from thermochromism affect the physical properties as well as the biological efficacy.

Contribution of Wound-Associated Cells and Mediators in Orchestrating Gastrointestinal Mucosal Wound Repair

The gastrointestinal mucosa, structurally formed by the epithelium and lamina propria, serves as a selective barrier that separates luminal contents from the underlying tissues. Gastrointestinal mucosal wound repair is orchestrated by a series of spatial and temporal events that involve the epithelium, recruited immune cells, resident stromal cells, and the microbiota present in the wound bed. Upon injury, repair of the gastrointestinal barrier is mediated by collective migration, proliferation, and subsequent differentiation of epithelial cells. Epithelial repair is intimately regulated by a number of wound-associated cells that include immune cells and stromal cells in addition to mediators released by luminal microbiota. The highly regulated interaction of these cell types is perturbed in chronic inflammatory diseases that are associated with impaired wound healing. An improved understanding of prorepair mechanisms in the gastrointestinal mucosa will aid in the development of novel therapeutics that promote mucosal healing and reestablish the critical epithelial barrier function.

IL-10 produced by macrophages regulates epithelial integrity in the small intestine

Macrophages (Mϕs) are known to be major producers of the anti-inflammatory cytokine interleukin-10 (IL-10) in the intestine, thus playing an important role in maintaining gastrointestinal homeostasis. Mϕs that reside in the small intestine (SI) have been previously shown to be regulated by dietary antigens, while colonic Mϕs are regulated by the microbiota. However, the role which resident Mϕs play in SI homeostasis has not yet been fully elucidated. Here, we show that SI Mϕs regulate the integrity of the epithelial barrier via secretion of IL-10. We used an animal model of non-steroidal anti-inflammatory drug (NSAID)-induced SI epithelial injury to show that IL-10 is mainly produced by MHCII⁺ CD64⁺ Ly6C^low Mϕs early in injury and that it is involved in the restoration of the epithelial barrier. We found that a lack of IL-10, particularly its secretion by Mϕs, compromised the recovery of SI epithelial barrier. IL-10 production by MHCII⁺ CD64⁺ Ly6C^low Mϕs in the SI is not regulated by the gut microbiota, hence depletion of the microbiota did not influence epithelial regeneration in the SI. Collectively, these results highlight the critical role IL-10-producing Mϕs play in recovery from intestinal epithelial injury induced by NSAID.

Silk fibroin nanoparticles as biocompatible nanocarriers of a novel light-responsive CO-prodrug

[Mn(CO)₃(2,2'-bipyridine)(PPh₃)](ClO₄) (1), a novel photoactive CO-releasing molecule, has been prepared and fully characterized. Besides, silk fibroin nanoparticles (SFNs) have been used, for the first time, as vehicles of 1 leading to the hybrid material 1@SFNs that shows an enhanced CO-delivery.

Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases. The procedure for getting the SMILES out of the CIF files starts with checking whether the atoms in the asymmetric unit are a chemically acceptable image of the compound. When they are not (molecule in a symmetry element, disorder, polymeric species,etc.), the previously published cif_molecule program is used to get such image in many cases. The program package Open Babel is then applied to get SMILES strings from the CIF files (either those directly taken from the COD or those produced by cif_molecule when applicable). The results are then checked and/or fixed by a human editor, in a computer-aided task that at present still consumes a great deal of human time. Even if the procedure still needs to be improved to make it more automatic (and hence faster), it has already yielded more than 160,000 curated chemical structures and the purpose of this article is to announce the existence of this work to the chemical community as well as to spread the use of its results.

Mesoxalate as Cu(ii)–Ln(iii) linker in the construction of MOFs in DMSO/water medium

The combination of [Cu₃(Hmesox)₃]³⁻ with La(iii), Ce(iii), Pr(iii), Nd(iii) and Eu(iii) in DMSO/H₂O yields 3d–4f heterometallic metal–organic frameworks, with the dimensionality of the network being controlled by the coordination number of the Ln(iii) ion.

Triazolopyrimidine compounds containing first-row transition metals and their activity against the neglected infectious Chagas disease and leishmaniasis

Leishmaniasis and Chagas disease remain a significant global problem. Current treatments have serious disadvantage due to cost, toxicity, long therapy duration and resistance. In the last years increasing interest has arisen in drug development to fight both diseases. Recently, metal-based drugs have revealed as promising drugs in a variety of therapeutic areas. Herein we describe six newly synthesized transition metal complexes with a bioactive molecule 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp). All of them have been characterized by X-ray, spectroscopic and thermal methods. In vitro and in vivo studies (murine model) on the antiproliferative activity of these complexes against Leishmania spp. (Leishmania infantum, Leishmania braziliensis) and Trypanosoma cruzi have been carried out. Our results reveal a strong potential of three of the assayed compounds as antiparasitic agents against the above-mentioned infectious diseases.

IFNγ-induced suppression of β-catenin signaling: evidence for roles of Akt and 14.3.3ζ

Nuclear Akt1 phosphorylates 14.3.3ζ at serine 58 to inhibit β-catenin transactivation. The results outline a dual function of Akt1, which suppresses intestinal epithelial cell proliferation during intestinal inflammation.

The proinflammatory cytokine interferon γ (IFNγ ) influences intestinal epithelial cell (IEC) homeostasis in a biphasic manner by acutely stimulating proliferation that is followed by sustained inhibition of proliferation despite continued mucosal injury. β-Catenin activation has been classically associated with increased IEC proliferation. However, we observed that IFNγ inhibits IEC proliferation despite sustained activation of Akt/β-catenin signaling. Here we show that inhibition of Akt/β-catenin–mediated cell proliferation by IFNγ is associated with the formation of a protein complex containing phosphorylated β-catenin 552 (pβ-cat552) and 14.3.3ζ. Akt1 served as a bimodal switch that promotes or inhibits β-catenin transactivation in response to IFNγ stimulation. IFNγ initially promotes β-catenin transactivation through Akt-dependent C-terminal phosphorylation of β-catenin to promote its association with 14.3.3ζ. Augmented β-catenin transactivation leads to increased Akt1 protein levels, and active Akt1 accumulates in the nucleus, where it phosphorylates 14.3.3ζ to translocate 14.3.3ζ/β-catenin from the nucleus, thereby inhibiting β-catenin transactivation and IEC proliferation. These results outline a dual function of Akt1 that suppresses IEC proliferation during intestinal inflammation.

H-bonds superstructures built by aquacomplexes and an azapurine derivative: a case of molecular recognition

The crystal structures of six compounds involving the divalent cations of Mn, Zn and Cd, the anionic form of the heterocycle 4,6-dimethyl-1,2,3-triazolo[4,5-d]pyrimidin-5,7-dione (Hdmax) and bipyridyl based spacer ligands are reported. The most important feature of these structures is the presence, in all cases, of a topologically identical 1-D polymeric superstructure (tape), involving tetra- or hexaaqua complex cations and triazolopyrimidine anions, built through hydrogen bonds. Adding these results to others previously published, we may consider these tapes as robust supramolecular synthons where a defined/clear case of molecular recognition between these two moieties takes place.

Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration

Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

ZO proteins and redox-dependent processes

SIGNIFICANCE

ZO-1, ZO-2, and ZO-3 are scaffold proteins of the tight junction (TJ) that belong to the MAGUK protein family characterized for exhibiting PDZ, SH3, and GuK domains. ZO proteins are present only in multicellular organisms, being the placozoa the first to have them. ZO proteins associate among themselves and with other integral and adaptor proteins of the TJ, of the ZA and of gap junctions, as with numerous signaling proteins and the actin cytoskeleton. ZO proteins are also present at the nucleus of proliferating cells.

RECENT ADVANCES

Oxidative stress disassembles the TJs of endothelial and epithelial cells.

CRITICAL ISSUES

Oxidative stress alters ZO proteins expression and localization, in conditions like hypoxia, bacterial and viral infections, vitamin deficiencies, age-related diseases, diabetes and inflammation, alcohol and tobacco consumption.

FUTURE DIRECTIONS

Molecules present in the signaling pathways triggered by oxidative stress can be targets for therapeutic intervention.

Bis(cyanato-κN)bis-(5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine-κN)zinc

In the title complex, [Zn(NCO)₂(C₇H₈N₄)₂], the Zn^II ion exhibits a distorted tetra­hedral coordination geometry. The coordination environment is formed by two 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp) ligands, coordinated through the N atom in position 3, and two cyanate anions inter­acting by their N atoms. Supra­molecular dimers are generated by stacking inter­actions between the pyrimidine rings of two ligands related by an inversion center [centroid–centroid distance = 3.5444 (18) Å].

Identification of claudins by western blot and immunofluorescence in different cell lines and tissues

Claudins are integral proteins of the TJ. Each epithelia in the organism expresses a unique set of claudins that determines the degree of sealing of the paracellular pathway and the ionic selectivity of the tissue. TJs are dynamic structures whose organization and composition change in response to alterations in the environment as well as under physiological and pathological conditions. Changes in claudin expression and subcellular distribution can be analyzed in western blot and immunofluorescence experiments, employing a wide array of available specific antibodies against claudins. In this chapter, we describe in detail protocols used for western blot and immunofluorescence detection of claudins in epithelial cell lines and in various tissue samples.

4,7-Phenanthrolinium perchlorate-5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7(4H)-one-water (1/1/2)

The asymmetric unit of the title compound, C₁₂H₉N₂⁺·ClO₄⁻·C₆H₆N₄O·2H₂O, contains a monoprotonated 4,7-phenanthrolinium (47phen) cation, a perchlorate anion balancing its charge, a neutral mol­ecule of 5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7(4H)-one (HmtpO) and two inter­stitial water mol­ecules. In the crystal structure, the acidic H atoms of 47phenH⁺ and HmtpO form strong hydrogen bonds with the water mol­ecules, which in turn act as hydrogen-bond donors, forming links between them and towards the carbonyl O atom of HmtpO, the non-protonated N atom of 47phen⁺ and one of the O atoms of the anion.

Versatile binding behaviour of 4,6-dimethyl-1,2,3-triazolo[4,5-d]-pyrimidin-5,7-dionato in the presence of bipyrimidine. Supramolecular H-bond architectures

Complexes with the ligand 4,6-dimethyl-1,2,3-triazolo-[4,5-d]-pyrimidin-5,7-dionato (dmax(-)) and the auxiliary chelating-bridging ligand bipyrimidine (bpym) have been synthesized and structurally characterized for the divalent cations of Zn, Cd and Cu. For Zn and Cd, dinuclear complexes with the formulae [Zn(2)(dmax)(4)(H(2)O)(2)(bpym)].2H(2)O and [Cd(2)(dmax)(4)(H(2)O)(4)(bpym)].6H(2)O have been isolated whereas for Cu, the one-dimensional polymer {[Cu(2)(dmax)(4)(bpym)].5H(2)O}(n) has been obtained. Bpym acts as a chelating-bridging ligand in the three compounds, joining couples of metal ions. Two crystallographically and chemically different dmax(-) ligands are present in each of these complexes, one monodentately linked via the triazole N atom furthest from the pyrimidine ring (N2) and the other either monodentately linked via the triazole N atom closer to a carbonyl group (N1, Zn and Cd compounds) or in bridging N1-N2 mode (Cu compound), in the latter case generating an one-dimensional polymer with alternating bpym and (dmax)(2) bridges. The magnetic interaction across the bpym bridge gives rise to a strong antiferromagnetic interaction (2J = -201 cm(-1)), whereas that across the (dmax)(2) bridge is negligible and cannot be reliably determined (obscured by the strong one). The hydrogen bonds between water molecules and the triazolopyrimidine derivative build the 3-D structure of the compounds.

Copper (II) complexes of [1,2,4]triazolo [1,5-a]pyrimidine derivatives as potential anti-parasitic agents

Anti-proliferative effects are described for newly synthesised copper (II) complexes of two triazolo-pyrimidine derivatives (1,2,4-triazolo-[1,5-a]pyrimidine, tp, and 5,7-dimethyl 1,2,4-triazolo-[1,5-a]pyrimidine, dmtp) against to Trypanosoma cruzi and Leishmania (Viannia) peruviana. Of the compounds assayed, those that presented the ligand tp and auxiliary ligand 1,10-phenanthroline (C24b, C49) were most highly active against to T. cruzi with IC(50) within the range of the reference drug benznidazole. These compounds, together with C35 were the most effective against L. (V.) peruviana with an IC(50) greater than that presented by reference drugs (Pentostam and Glucantim). These compounds were not toxic to the host cell. IC(25) diminished the infection capacity and severely reduced the multiplication of intracellular forms of T. cruzi, and L. (V.) peruviana. In the case of T. Cruzi, the transformation to trypomastigote was seriously depressed. Copper (II) complexes C24b, C49 and C35, acted on the energy metabolism of the parasites at the level of the NAD(+)/NADH balance and at the level of the organelle membranes, causing degradation and cell death.

Crystallography Open Database - an open-access collection of crystal structures

The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal–organic and small organic molecule structures in one database, providing a straightforward search and retrieval interface. The COD adopts an open-access model for its >80 000 structure files.

The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

Synthesis, structure and biological activity of a new and efficient Cd(II)–uracil derivative complex system for cleavage of DNA

The new complex formed by Cd(II) and the 1:2 Schiff-base-type ligand 2,6-bis[1-(4-amino-1,2,3,6-tetrahydro-1,3-dimethyl-2,6-dioxopyrimidin-5-yl)imino]ethylpyridine (DAPDAAU) has been chemically and structurally characterized by X-ray diffraction: the ion Cd(II) is surrounded by six nitrogen atoms from two DAPDAAU ligands which coordinates each one in a tridentate fashion through the pyridine ring (N1) and both azomethine nitrogen atoms (N5). The interaction of the Cd(II) complex (compound I) with calf-thymus DNA as observed by circular dichroism spectroscopy suggests the initial unwinding of the DNA double helix strongly depends on increasing incubation times and metal-to-nucleic acid molar ratios. Electrophoretic experiments indicate that the cadmium complex induces cleavage of the plasmid pBR322 DNA to give ulterior nicking and shortening of this molecule, as a result of the complex binding to DNA, resulting in the conclusion that compound I behaves as a chemical nuclease. Cytotoxic activity of the Cd(II) complex against selected different human cancer cell lines is specific and increases with increasing concentration of the metal compound; this fact indicates the potential antitumor character of the complex. When the culture medium is supplemented with compound I, a remarkable inhibition of the growing cell is observed, important cell degeneration appears before 48 h and abundant precipitates are formed that correspond to cell residues and denatured proteins.

Cellular and subcellular localization of endogenous nitric oxide in young and senescent pea plants

The cellular and subcellular localization of endogenous nitric oxide (NO.) in leaves from young and senescent pea (Pisum sativum) plants was studied. Confocal laser scanning microscopy analysis of pea leaf sections with the fluorescent probe 4,5-diaminofluorescein diacetate revealed that endogenous NO. was mainly present in vascular tissues (xylem and phloem). Green fluorescence spots were also detected in the epidermal cells, palisade and spongy mesophyll cells, and guard cells. In senescent leaves, NO. generation was clearly reduced in the vascular tissues. At the subcellular level, by electron paramagnetic resonance spectroscopy with the spin trap Fe(MGD)(2) and fluorometric analysis with 4,5-diaminofluorescein diacetate, NO. was found to be an endogenous metabolite of peroxisomes. The characteristic three-line electron paramagnetic resonance spectrum of NO., with g = 2.05 and a(N) = 12.8 G, was detected in peroxisomes. By fluorometry, NO. was also found in these organelles, and the level measured of NO. was linearly dependent on the amount of peroxisomal protein. The enzymatic production of NO. from l-Arg (nitric oxide synthase [NOS]-like activity) was measured by ozone chemiluminiscence. The specific activity of peroxisomal NOS was 4.9 nmol NO. mg(-1) protein min(-1); was strictly dependent on NADPH, calmodulin, and BH(4); and required calcium. In senescent pea leaves, the NOS-like activity of peroxisomes was down-regulated by 72%. It is proposed that peroxisomal NO. could be involved in the process of senescence of pea leaves.

Mononucleotide recognition by cyclic trinuclear palladium(II) complexes containing 4,7-phenanthroline N,N bridges

Reaction of [(dach)Pd(NO3)2] entities (dach = (R,R)-1,2-diaminocyclohexane, (S,S)-1,2-diaminocyclohexane) and 4,7-phenanthroline (phen) providing, respectively, 90 and 120 degrees bond angles, leads to the formation of two novel positively charged homochiral cyclic trinuclear metallacalix[3]arene species [((R,R)-1,2-diaminocyclohexane)Pd(phen)]3(NO3)6 (2a) and [((S,S)-1,2-diaminocyclohexane)Pd(phen)]3(NO3)6 (2b). These species have been characterised by 1)H NMR and X-ray diffraction methods (2b), showing that they possess accessible cavities suited for supramolecular recognition processes. We prove, indeed, from 1H NMR studies the inclusion of mononucleotides inside the cavity of the trinuclear species [(ethylenediamino)Pd(phen)]3(6+) (1), [((R,R)-1,2-diaminocyclohexane)Pd(phen)]3(6+) (2a) and [((S,S)-1,2-diaminocyclohexane)Pd(phen)]3(6+) (2b) in aqueous solution. Association constants (K(ass)) range from 85 +/- 6 M(-1) for the interaction between [(ethylenediamine)Pd(phen)]3(6+) and adenosine monophosphate to 37 +/- 4 M(-1) for the interaction between [(1,2-diaminocyclohexane)Pd(phen)]3(6+) and thymidine monophosphate. We invoke the synergy of electrostatic, anion-pi and pi-pi interactions to explain the recognition of mononucleotides inside the cavity of the metallacalix[3]arenes.

Chiral Pyrimidine Metallacalixarenes: Synthesis, Structure and Host–Guest Chemistry

A set of enantiomerically pure cyclic multinuclear complexes with the formula cis-[a(2)PdL](n) (n+) [a(2)=(R,R)-1,2-diaminocyclohexane (R,R-dach), (S,S)-1,2-diaminocyclohexane (S,S-dach); n=4, 6; LH=2-hydroxypyrimidine (2-Hpymo), 4,6-dimethyl-2-hydroxypyrimidine (2-Hdmpymo) and 4-hydroxypyrimidine (4-Hpymo)] were obtained by reaction of cis-[a(2)Pd(H(2)O)(2)](2+) and LH in aqueous media. The polynuclear complexes were studied by (1)H NMR spectroscopy and X-ray crystallography. These studies revealed that the N1,N3-bridging mode exhibited by the pyrimidine moieties is ideally suited for formation of inorganic analogues of calixarenes (metallacalixarenes) in a self-assembly process. The most stable species are the tetranuclear metallacalix[4]arenes, which are obtained in all cases. Hexanuclear species, namely, [a(2)Pd(2-dmpymo)](6) (6+), were also isolated and fully characterised. (1)H NMR experiments show conversion of [a(2)Pd(2-dmpymo)](6) (6+) to [a(2)Pd(2-dmpymo)](4) (4+) on heating. Analogously to organic calixarenes, these systems are also capable of incorporating hard metal ions at the oxo surface. Additionally, investigations on the receptor properties of these metallacalixarenes towards mononucleotides showed that enantioselective recognition processes occur in aqueous media.