Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

Background Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Results Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. Conclusions 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch webcite and should provide useful assistance to drug discovery projects.

Interactions and structural analysis of the zinc -binding motif in decorin, a small leucine rich proteoglycan in extracellular matrix

Decorin, a dermatan/chondroitin sulfate proteoglycan, is ubiquitously distributed in the extracellular matrix (ECM) of mammals. Decorin belongs to the small leucine rich proteoglycan (SLRP) family, a proteoglycan family characterized by a core protein dominated by Leucine Rich Repeat motifs. The decorin core protein appears to mediate the binding of decorin to ECM molecules, such as collagens and fibronectin. It is believed that the interactions of decorin with these ECM molecules contribute to the regulation of ECM assembly, cell adhesions, and cell proliferation. These basic biological processes play critical roles during embryonic development and wound healing and are altered in pathological conditions such as fibrosis and tumorgenesis. ^ In this dissertation, we discover that decorin core protein can bind to Zn2+ ions with high affinity. Zinc is an essential trace element in mammals. Zn2+ ions play a catalytic role in the activation of many enzymes and a structural role in the stabilization of protein conformation. By examining purified recombinant decorin and its core protein fragments for Zn2+ binding activity using Zn2+-chelating column chromatography and Zn2+-equilibrium dialysis approaches, we have located the Zn2+ binding domain to the N-terminal sequence of the decorin core protein. The decorin N-terminal domain appears to contain two Zn2+ binding sites with similar high binding affinity. The sequence of the decorin N-terminal domain does not resemble any other reported zinc-binding motifs and, therefore, represents a novel Zn 2+ binding motif. By investigating the influence of Zn2+ ions on decorin binding interactions, we found a novel Zn2+ dependent interaction with fibrinogen, the major plasma protein in blood clots. Furthermore, a recombinant peptide (MD4) consisting of a 41 amino acid sequence of mouse decorin N-terminal domain can prolong thrombin induced fibrinogen/fibrin clot formation. This suggests that in the presence of Zn2+ the decorin N-terminal domain has an anticoagulation activity. The changed Zn2+-binding activities of the truncated MD4 peptides and site-directed mutagenesis generated mutant peptides revealed that the functional MD4 peptide might contain both a structural zinc-binding site in the cysteine cluster region and a catalytic zinc site that could be created by the flanking sequences of the cysteine cluster region. A model of a loop-like structure for MD4 peptide is proposed. ^

Glyphosate, Manganese, and Zinc Soybean Trial

Often there is yellowing of soybeans following glyphosate applications that has been attributed by some as manganese or zinc deficiency. There have been varied reports of impacts of this ‘yellow flash’ on soybean yields. The trial was conducted to investigate such claims.

The distribution of zinc, cadmium, copper and iron in seawater of the Iceland-Faroe Ridge area

During the International ICES Expedition "Overflow '73" a total of 174 samples from 18 stations were collected by R. V. "Meteor" in the waters of the Iceland-Faroe Ridge area. They were filtered on board ship (through 0.4 mym "Nuclepore" filters), then stored in 500 cm**3 quartz bottles (at -20 °C) and analyzed in air-filtered laboratories on land for zinc and cadmium by means of the differential pulse anodic stripping voltammetry technique and copper and iron by flameless atomic absorption spectrometry. The overall averages of 1.9 myg Zn l**-1, 0.07 myg Cd l**-1, 0.5 myg Cu l**-1 and 0.9 myg Fe l**-1 are in good agreement with recent "baseline" studies of open-ocean waters. The mixture of low salinity water masses from the North Iceland Shelf/Arctic Intermediate Waters seem to maintain distinctly lower concentration of Cd, Cu and Fe than the waters from the North Atlantic and the Norwegian Sea where quite similar mean values are found. There is only little evidence for the assumption that overflow events on the ridge are influencing the concentrations of dissolved metals in the near-bottom layers.

Whole-rock and mineral geochemistry of ODP Hole 176-735B gabbros

We report mineral chemistry, whole-rock major element compositions, and trace element analyses on Hole 735B samples drilled and selected during Leg 176. We discuss these data, together with Leg 176 shipboard data and Leg 118 sample data from the literature, in terms of primary igneous petrogenesis. Despite mineral compositional variation in a given sample, major constituent minerals in Hole 735B gabbroic rocks display good chemical equilibrium as shown by significant correlations among Mg# (= Mg/[Mg + Fe2+]) of olivine, clinopyroxene, and orthopyroxene and An (=Ca/[Ca + Na]) of plagioclase. This indicates that the mineral assemblages olivine + plagioclase in troctolite, plagioclase + clinopyroxene in gabbro, plagioclases + clinopyroxene + olivine in olivine gabbro, and plagioclase + clinopyroxene + olivine + orthopyroxene in gabbronorite, and so on, have all coprecipitated from their respective parental melts. Fe-Ti oxides (ilmenite and titanomagnetite), which are ubiquitous in most of these rocks, are not in chemical equilibrium with olivine, clinopyroxene, and plagioclase, but precipitated later at lower temperatures. Disseminated oxides in some samples may have precipitated from trapped Fe-Ti-rich melts. Oxides that concentrate along shear bands/zones may mark zones of melt coalescence/transport expelled from the cumulate sequence as a result of compaction or filter pressing. Bulk Hole 735B is of cumulate composition. The most primitive olivine, with Fo = 0.842, in Hole 735B suggests that the most primitive melt parental to Hole 735B lithologies must have Mg# 0.637, which is significantly less than Mg# = 0.714 of bulk Hole 735B. This suggests that a significant mass fraction of more evolved products is needed to balance the high Mg# of the bulk hole. Calculations show that 25%-45% of average Eastern Atlantis II Fracture Zone basalt is needed to combine with 55%-75% of bulk Hole 735B rocks to give a melt of Mg# 0.637, parental to the most primitive Hole 735B cumulate. On the other hand, the parental melt with Mg# 0.637 is far too evolved to be in equilibrium with residual mantle olivine of Fo > 0.89. Therefore, a significant mass fraction of more primitive cumulate (e.g., high Mg# dunite and troctolite) is yet to be sampled. This hidden cumulate could well be deep in the lower crust or simply in the mantle section. We favor the latter because of the thickened cold thermal boundary layer atop the mantle beneath slow-spreading ridges, where cooling and crystallization of ascending mantle melts is inevitable. These observations and data interpretation require reconsideration of the popular concept of primary mantle melts and relationships among the extent of mantle melting, melt production, and the composition and thickness of igneous crust.

Concentrations of As and other chemical elements in bottom sediments of the Baltic Sea

As is less toxic than Hg, Cd, Pb, Se, Zn, and Cu. The As clarke for clays and shales is 10 ppm. Our samples of bottom sediments from Kurshskii Bay were determined to contain from 15 to 26 ppm As and up to 34 ppm As in the vicinity of the Neman River mouth. Elevated As concentrations (50-114 ppm) were detected in four columns of subsurface bottom sediments (at depths of 10-65 cm) from the Vistula Lagoon. Elevated As concentrations (50-180 ppm) were also found in a few surface samples of sand from the Gdansk Deep near oil platform D-6. These sediments are either partly contaminated with anthropogenic As or contain Fe sulfides and glauconite, which can concentrate As and contain its elevated concentrations. The As concentration in columns of bottom sediments from the Gulf of Finland were at the natural background level (throughout the columns) typical of the area (9-34 ppm). We repeatedly detected very high As concentrations (up to 227 ppm As) in politic ooze from Bornholm Deep, in the vicinity of the sunken vessel with chemical weapons. The sources of elevated As concentrations in the Baltic Sea are the following: (1) chemical weapon (CW) material buried in the floor of the Baltic Sea; (2) As-bearing pesticides, agricultural mineral fertilizers, and burned coal and other fuels; (3) kerogen-bearing Ordovician rocks exposed on the bottom; and (4) As-rich Fe sulfides brought to the area together with construction sand and gravel. This mixture was used in paper production and for the construction of hydraulic engineering facilities in the Vistula Lagoon in the early 20th century and later caused the so-called lagoon disease.

Thermodynamics of zinc insertion in CuGaS2:Ti, used as a modulator agent in an intermediate-band photovoltaic material

An intermediate-bandphotovoltaicmaterial, which has an isolated metallic band located between the top of the valence band and bottom of the conduction band of some semiconductors, has been proposed as third generation solar cell to be used in photovoltaic applications. Density functional theory calculations of Zn in CuGaS2:Ti have previously shown that, the intermediate-band position can be modulated in proportion of Zn insertion in such a way that increasing Zn concentration can lead to aband-gap reduction, and an adjustment of the intermediate-band position. This could be interesting in the formation of an intermediate-bandmaterial, that has the maximum efficiency theoretically predicted for the intermediate-band solar cell. In this work, the energetics of several reaction schemes that could lead to the decomposition of the modulated intermediate-bandphotovoltaicmaterial, CuGaS2:Ti:Zn, is studied in order to assess the thermodynamic stability of this material. Calculations of the total free energy and disorder entropy have been taken into account, to get the reaction energy and free energy of the compound decomposition, which is found to be thermodynamically favorable

Residual effect of natural and synthetic zinc chelates on zinc in a soil solution of a waterlogged acidic soil. Evolution of the pH and redox potential.

Zinc chelates have been widely used to correct deficiencies in this micronutrient in different soil types and under different moisture conditions. The aging of the metal in soil could cause a change in its availability. Over time the most labile forms of Zn could decrease in activity and extractability and change to more stable forms. Various soil parameters, such as redox conditions, time, soil type and moisture conditions, affect the aging process and modify the solubility of the metal. In general, redox conditions influence pH and also the chemical forms dissolved in the soil solution. Soil pH also affects Zn solubility; at high pH values, most of the Zn is present in forms that are not bioavailable to plants. The objective of this study was to determine the changes in Zn over time in a soil solution in a waterlogged acidic soil to which synthetic and natural chelates were applied

Importancia de una correcta fertilización de zinc en el cultivo de lino.

Almendros, P.; Alvarez, J.M.; Gonzalez, D.

Residual effect of organic zinc complexes in acid and calcareous soils on navy bean (phaseolus vulgaris l.) and flax (linum usitatissimum l.) crops under greenhouse conditions. Influence of the moisture conditions = Efecto residual de complejos orgánicos de zinc en suelos ácido y calizo en cultivos de judía (phaseolus vulgaris l.) y lino (linum usitatissimum l.) Realizados en condiciones de invernadero. Influencia de las diferentes condiciones de humedad

El Zn es un elemento esencial para el crecimiento saludable y reproducción de plantas, animales y humanos. La deficiencia de Zn es una de las carencias de micronutrientes más extendidas en muchos cultivos, afectando a grandes extensiones de suelos en diferentes áreas agrícolas. La biofortificación agronómica de diferentes cultivos, incrementando la concentración de micronutriente Zn en la planta, es un medio para evitar la deficiencia de Zn en animales y humanos. Tradicionalmente se han utilizado fertilizantes de Zn inorgánicos, como el ZnSO4, aunque en los últimos años se están utilizado complejos de Zn como fuentes de este micronutriente, obteniéndose altas concentraciones de Zn soluble y disponible en el suelo. Sin embargo, el envejecimiento de la fuente en el suelo puede causar cambios importantes en su disponibilidad para las plantas. Cuando se añaden al suelo fuentes de Zn inorgánicas, las formas de Zn más solubles pierden actividad y extractabilidad con el paso del tiempo, transformándose a formas más estables y menos biodisponibles. En esta tesis se estudia el efecto residual de diferentes complejos de Zn de origen natural y sintético, aplicados en cultivos previos de judía y lino, bajo dos condiciones de riego distintas (por encima y por debajo de la capacidad de campo, respectivamente) y en dos suelos diferentes (ácido y calizo). Los fertilizantes fueron aplicados al cultivo previo en tres dosis diferentes (0, 5 y 10 mg Zn kg-1 suelo). El Zn fácilmente lixiviable se estimó con la extracción con BaCl2 0,1M. Bajo condiciones de humedad por encima de la capacidad de campo se obtuvieron mayores porcentajes de Zn lixiviado en el suelo calizo que en el suelo ácido. En el caso del cultivo de judía realizado en condiciones de humedad por encima de la capacidad de campo se compararon las cantidades extraídas con el Zn lixiviado real. El análisis de correlación entre el Zn fácilmente lixiviable y el estimado sólo fue válido para complejos con alta movilidad y para cada suelo por separado. Bajo condiciones de humedad por debajo de la capacidad de campo, la concentración de Zn biodisponible fácilmente lixiviable presentó correlaciones positivas y altamente significativas con la concentración de Zn disponible en el suelo. El Zn disponible se estimó con varios métodos de extracción empleados habitualmente: DTPA-TEA, DTPA-AB, Mehlich-3 y LMWOAs. Estas concentraciones fueron mayores en el suelo ácido que en el calizo. Los diferentes métodos utilizados para estimar el Zn disponible presentaron correlaciones positivas y altamente significativas entre sí. La distribución del Zn en las distintas fracciones del suelo fue estimada con diferentes extracciones secuenciales. Las extracciones secuenciales mostraron un descenso entre los dos cultivos (el anterior y el actual) en la fracción de Zn más lábil y un aumento en la concentración de Zn asociado a fracciones menos lábiles, como carbonatos, óxidos y materia orgánica. Se obtuvieron correlaciones positivas y altamente significativas entre las concentraciones de Zn asociado a las fracciones más lábiles (WSEX y WS+EXC, experimento de la judía y lino, respectivamente) y las concentraciones de Zn disponible, estimadas por los diferentes métodos. Con respecto a la planta se determinaron el rendimiento en materia seca y la concentración de Zn en planta. Se observó un aumento del rendimiento y concentraciones con el efecto residual de la dosis mayores (10 mg Zn kg-1) con respecto a la dosis inferior (5 mg Zn 12 kg-1) y de ésta con respecto a la dosis 0 (control). El incremento de la concentración de Zn en todos los tratamientos fertilizantes, respecto al control, fue mayor en el suelo ácido que en el calizo. Las concentraciones de Zn en planta indicaron que, en el suelo calizo, serían convenientes nuevas aplicaciones de Zn en posteriores cultivos para mantener unas adecuadas concentraciones en planta. Las mayores concentraciones de Zn en la planta de judía, cultivada bajo condiciones de humedad por encima de la capacidad de campo, se obtuvieron en el suelo ácido con el efecto residual del Zn-HEDTA a la dosis de 10 mg Zn kg-1 (280,87 mg Zn kg-1) y en el suelo calizo con el efecto residual del Zn-DTPA-HEDTA-EDTA a la dosis de 10 mg Zn kg-1 (49,89 mg Zn kg-1). En el cultivo de lino, cultivado bajo condiciones de humedad por debajo de la capacidad de campo, las mayores concentraciones de Zn en planta ese obtuvieron con el efecto residual del Zn-AML a la dosis de 10 mg Zn kg-1 (224,75 mg Zn kg-1) y en el suelo calizo con el efecto residual del Zn-EDTA a la dosis de 10 mg Zn kg-1 (99,83 mg Zn kg-1). El Zn tomado por la planta fue determinado como combinación del rendimiento y de la concentración en planta. Bajo condiciones de humedad por encima de capacidad de campo, con lixiviación, el Zn tomado por la judía disminuyó en el cultivo actual con respecto al cultivo anterior. Sin embargo, en el cultivo de lino, bajo condiciones de humedad por debajo de la capacidad de campo, se obtuvieron cantidades de Zn tomado superiores en el cultivo actual con respecto al anterior. Esta tendencia también se observó, en ambos casos, con el porcentaje de Zn usado por la planta. Summary Zinc is essential for healthy growth and reproduction of plants, animals and humans. Zinc deficiency is one of the most widespread micronutrient deficiency in different crops, and affect different agricultural areas. Agronomic biofortification of crops produced by an increased of Zn in plant, is one way to avoid Zn deficiency in animals and humans Sources with inorganic Zn, such as ZnSO4, have been used traditionally. Although, in recent years, Zn complexes are used as sources of this micronutrient, the provide high concentrations of soluble and available Zn in soil. However, the aging of the source in the soil could cause significant changes in their availability to plants. When an inorganic source of Zn is added to soil, Zn forms more soluble and extractability lose activity over time, transforming into forms more stable and less bioavailable. This study examines the residual effect of different natural and synthetic Zn complexes on navy bean and flax crops, under two different moisture conditions (above and below field capacity, respectively) and in two different soils (acid and calcareous). Fertilizers were applied to the previous crop in three different doses (0, 5 y 10 mg Zn kg-1 soil). The easily leachable Zn was estimated by extraction with 0.1 M BaCl2. Under conditions of moisture above field capacity, the percentage of leachable Zn in the calcareous soil was higher than in acid soil. In the case of navy bean experiment, performed in moisture conditions of above field capacity, amounts extracted of easily leachable Zn were compared with the real leachable Zn. Correlation analysis between the leachable Zn and the estimate was only valid for complex with high mobility and for each soil separately. Under moisture conditions below field capacity, the concentration of bioavailable easily leachable Zn showed highly significant positive correlations with the concentration of available soil Zn. The available Zn was estimated with several commonly used extraction methods: DTPA-TEA, AB-DTPA, Mehlich-3 and LMWOAs. These concentrations were higher in acidic soil than in the calcareous. The different methods used to estimate the available Zn showed highly significant positive correlations with each other. The distribution of Zn in the different fractions of soil was estimated with different sequential extractions. The sequential extractions showed a decrease between the two crops (the previous and current) at the most labile Zn fraction and an increase in the concentration of Zn associated with the less labile fractions, such as carbonates, oxides and organic matter. A positive and highly significant correlation was obtained between the concentrations of Zn associated with more labile fractions (WSEX and WS + EXC, navy bean and flax experiments, respectively) and available Zn concentrations determined by the different methods. Dry matter yield and Zn concentration in plants were determined in plant. Yield and Zn concentration in plant were higher with the residual concentrations of the higher dose applied (10 mg Zn kg-1) than with the lower dose (5 mg Zn kg-1), also these parameters showed higher values with application of this dose than with not Zn application. The increase of Zn concentration in plant with Zn treatments, respect to the control, was greater in the acid soil than in the calcareous. The Zn concentrations in plant indicated that in the calcareous soil, new applications of Zn are desirable in subsequent crops to maintain suitable concentrations in plant. 15 The highest concentrations of Zn in navy bean plant, performed under moisture conditions above the field capacity, were obtained with the residual effect of Zn-HEDTA at the dose of 10 mg Zn kg-1 (280.87 mg Zn kg-1) in the acid soil, and with the residual effect of Zn- DTPA-HEDTA-EDTA at a dose of 10 mg Zn kg-1 (49.89 mg Zn kg-1) in the calcareous soil. In the flax crop, performed under moisture conditions below field capacity, the highest Zn concentrations in plant were obtained with the residual effect of Zn-AML at the dose of 10 mg Zn kg-1 (224.75 Zn mg kg-1) and with the residual effect of Zn-EDTA at a dose of 10 mg Zn kg-1 (99.83 mg Zn kg-1) in the calcareous soil. The Zn uptake was determined as a combination of yield and Zn concentration in plant. Under moisture conditions above field capacity, with leaching, Zn uptake by navy bean decreased in the current crop, respect to the previous crop. However, in the flax crop, under moisture conditions below field capacity, Zn uptake was higher in the current crop than in the previous. This trend is also observed in both cases, with the percentage of Zn used by the plant

Chemical speciation and mobilization of copper and zinc in naturally contaminated mine soils with citric and tartaric acids

A one-step extraction procedure and a leaching column experiment were performed to assess the effects of citric and tartaric acids on Cu and Zn mobilization in naturally contaminated mine soils to facilitate assisted phytoextraction. A speciation modeling of the soil solution and the metal fractionation of soils were performed to elucidate the chemical processes that affected metal desorption by organic acids. Different extracting solutions were prepared, all of which contained 0.01 M KNO3 and different concentrations of organic acids: control without organic acids, 0.5 mM citric, 0.5 mM tartaric, 10 mM citric, 10 mM tartaric, and 5 mM citric +5 mM tartaric. The results of the extraction procedure showed that higher concentrations of organic acids increased metal desorption, and citric acid was more effective at facilitating metal desorption than tartaric acid. Metal desorption was mainly influenced by the decreasing pH and the dissolution of Fe and Mn oxides, not by the formation of soluble metal–organic complexes as was predicted by the speciation modeling. The results of the column study reported that low concentrations of organic acids did not significantly increase metal mobilization and that higher doses were also not able to mobilize Zn. However, 5–10 mM citric acid significantly promoted Cu mobilization (from 1 mg kg−1 in the control to 42 mg kg−1 with 10 mM citric acid) and reduced the exchangeable (from 21 to 3 mg kg−1) and the Fe and Mn oxides (from 443 to 277 mg kg−1) fractions. Citric acid could efficiently facilitate assisted phytoextraction techniques.