Development of a natural products database from the biodiversity of Brazil

We describe herein the design and development of an innovative tool called the NuBBE database (NuBBEDB), a new Web-based database, which incorporates several classes of secondary metabolites and derivatives from the biodiversity of Brazil. This natural product database incorporates botanical, chemical, pharmacological, and toxicological compound information. The NuBBEDB provides specialized information to the worldwide scientific community and can serve as a useful tool for studies on the multidisciplinary interfaces related to chemistry and biology, including virtual screening, dereplication, metabolomics, and medicinal chemistry. The NuBBEDB site is at http://nubbe.iq.unesp.br/nubbeDB.html. © 2013 The American Chemical Society and American Society of Pharmacognosy.

Trioctahedral micas in xenolithic ejecta from recent volcanism of the Somma-Vesuvius

This study reports the first crystal chemical database resulting from a detailed structural investigation of trioctahedral micas found in xenolithic ejecta produced during the AD 1631, 1872 and 1944 eruptions, three explosive episodes of recent volcanic period of Vesuvius volcano (Southern Italy). Three xenolith types were selected: metamorphic/metasomatic skarns, pyrometamorphic/hydrothermally altered nodules and mafic cumulates. They are related to different magma chemistry and effusive styles: from sub-plinian and most evolved (AD 1631 eruption) to violent strombolian with medium evolution degree (AD 1872 eruption) to vulcanian-effusive, least evolved (AD 1944 eruption) event, respectively. Both xenoliths and micas were investigated employing multiple techniques: the xenoliths were characterized by X-ray fluorescence, inductively-coupled plasma-mass spectrometry, optical microscopy, X-ray powder diffraction, and quantitative energy-dispersive microanalysis; the micas were studied by electron probe microanalysis and single crystal X-ray diffraction. The mica-bearing xenoliths show variable texture and mineralogical assemblage, clearly related to their different origin. Based on the major oxide chemistry, only one xenolithic sample falls in the skarn compositional field from the Somma-Vesuvius literature, some fall close to the skarns and cumulate fields, others plot close to the syenite/foidolite/essexite field. A subgroup of the selected ejecta does not fall or approach any of the compositional fields. Trace and rare earth element patterns show some petrological affinity between studied xenoliths and erupted magmas with typical Eu, Ta and Nb negative anomalies. Strongly depleted patterns were detected for the 1631 metamorphic/metasomatic skarns xenoliths. Three distinct mica groups were distinguished: 1) Mg-, Al-rich, low Ti-bearing, low to moderate F-bearing varieties (1631 xenolith), 2) Al-moderate, F- and Mg-rich, Ti-, Fe-poor varieties (1872 xenolith), and 3) Al-, Ti- and Fe-rich, F-poor phases (1944 xenolith). All the analysed mica crystals are 1M polytypes with the expected space group C2/m. Micas from xenoliths of the 1631 Vesuvius eruption are phlogopites characterized by a combination of low extent of oxy-type and variable extent OH-F-substitutions, as testified by the range of F concentration (from ~ 0.20 to 0.80 apfu). Micas from xenoliths of the 1872 Vesuvius eruption exhibit structural peculiarities typical of fluorophlogopites, i.e. OH-F-substitution is predominant. Micas from the xenolith of the 1944 Vesuvius eruption display features typical of oxy-substituted micas. The variability of the crystal chemical features of the studied micas are consistent with the remarkable variation of their host rocks. Micas from 1631 nodules are related to metasomatic, skarn-type environment, deriving from the metamorphosed wall-rocks hosting the magma reservoir. The fluorophlogopites from the 1872 xenoliths testify for strongly dehydrated environmental conditions compared to those of the 1631 and 1944 hosts. Finally, magma storage condition at depth, associated to a decreasing aH2O may have promoted major oxy-type substitutions in 1944 biotites.

A new database compilation of whole-rock chemical and geochronological data of igneous rocks in Queensland : a new resource for HDR geothermal resource exploration

The Geothermal industry in Australia and Queensland is in its infancy and for hot dry rock (HDR) geothermal energy, it is very much in the target identification and resource definition stages. As a key effort to assist the geothermal industry and exploration for HDR in Queensland, we are developing a comprehensive and new integrated geochemical and geochronological database on igneous rocks. To date, around 18,000 igneous rocks have been analysed across Queensland for chemical and/or age information. However, these data currently reside in a number of disparate datasets (e.g., Ozchron, Champion et al., 2007, Geological Survey of Queensland, journal publications, and unpublished university theses). The goal of this project is to collate and integrate these data on Queensland igneous rocks to improve our understanding of high heat producing granites in Queensland, in terms of their distribution (particularly in the subsurface), dimensions, ages, and controlling factors in their genesis.

Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

Identification of selective norbornane-type aspartate analogue inhibitors of the glutamate transporter 1 (GLT-1) from the chemical universe generated database (GDB)

A variety of conformationally constrained aspartate and glutamate analogues inhibit the glutamate transporter 1 (GLT-1, also known as EAAT2). To expand the search for such analogues, a virtual library of aliphatic aspartate and glutamate analogues was generated starting from the chemical universe database GDB-11, which contains 26.4 million possible molecules up to 11 atoms of C, N, O, F, resulting in 101026 aspartate analogues and 151285 glutamate analogues. Virtual screening was realized by high-throughput docking to the glutamate binding site of the glutamate transporter homologue from Pyrococcus horikoshii (PDB code: 1XFH ) using Autodock. Norbornane-type aspartate analogues were selected from the top-scoring virtual hits and synthesized. Testing and optimization led to the identification of (1R*,2R*,3S*,4R*,6R*)-2-amino-6-phenethyl-bicyclo[2.2.1]heptane-2,3-dicarboxylic acid as a new inhibitor of GLT-1 with IC(50) = 1.4 ?M against GLT-1 and no inhibition of the related transporter EAAC1. The systematic diversification of known ligands by enumeration with help of GDB followed by virtual screening, synthesis, and testing as exemplified here provides a general strategy for drug discovery.