Robust cross-validation of linear regression QSAR models

A quantitative structure-activity relationship (QSAR) model is typically developed to predict the biochemical activity of untested compounds from the compounds' molecular structures. "The gold standard" of model validation is the blindfold prediction when the model's predictive power is assessed from how well the model predicts the activity values of compounds that were not considered in any way during the model development/calibration. However, during the development of a QSAR model, it is necessary to obtain some indication of the model's predictive power. This is often done by some form of cross-validation (CV). In this study, the concepts of the predictive power and fitting ability of a multiple linear regression (MLR) QSAR model were examined in the CV context allowing for the presence of outliers. Commonly used predictive power and fitting ability statistics were assessed via Monte Carlo cross-validation when applied to percent human intestinal absorption, blood-brain partition coefficient, and toxicity values of saxitoxin QSAR data sets, as well as three known benchmark data sets with known outlier contamination. It was found that (1) a robust version of MLR should always be preferred over the ordinary-least-squares MLR, regardless of the degree of outlier contamination and that (2) the model's predictive power should only be assessed via robust statistics. The Matlab and java source code used in this study is freely available from the QSAR-BENCH section of www.dmitrykonovalov.org for academic use. The Web site also contains the java-based QSAR-BENCH program, which could be run online via java's Web Start technology (supporting Windows, Mac OSX, Linux/Unix) to reproduce most of the reported results or apply the reported procedures to other data sets.     

Chemoenzymatic acylation of aminoglycoside antibiotics

The chemoenzymatic installation of the clinically valuable (S)-4-amino-2-hydroxybutyryl side chain onto a number of 2-deoxystreptamine-containing aminoglycosides is described using the purified Bacillus circulans biosynthetic enzymes BtrH and BtrG in combination with a synthetic acyl-SNAC surrogate substrate.     

Prediction of the conditions for breathing of metal organic framework materials using a combination of X-ray powder diffraction, microcalorimetry, and molecular simulation

The adsorption of C1 to C4 linear hydrocarbons in the flexible metal organic framework MIL-53(Cr) has been followed by adsorption manometry coupled with microcalorimetry and Synchrotron X-ray powder diffraction. This experimental investigation was completed by molecular modeling. In the case of methane, the solid remains rigid whatever the adsorbate amount. However for the C2-C4 series, an increasing flexibility of the structure is observed, which is ascribed first to a breathing of the material from a large pore to a narrow pore form followed by a further expansion at high pressure. The collected thermodynamic and structural information suggests that a minimum adsorption enthalpy of ca. 20 kJ mol (-1) in the initial large pore structure of MIL-53(Cr) is required to induce the structural transition "large to narrow pore". Further, the enthalpy of adsorption can be used to predict the pressure at which the structure reopens. Finally, the magnitude of the breathing can be related to the size of the probe molecule via the van der Waals volume. The above trends have been successfully verified in the case of water and carbon dioxide. This combined experimental and theoretical approach gives the first elements for the prediction of whether or not the MIL53 and similar flexible structures will respond to gas loading and what would be the pressure required and further the amplitude of the induced breathing.     

Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain

Butirosin, an aminoglycoside antibiotic produced by Bacillus circulans, bears the unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain, which protects the antibiotic from several common resistance mechanisms. The AHBA side chain is advantageously incorporated into clinically valuable antibiotics such as amikacin and arbekacin by synthetic methods. Therefore, it is of significant interest to explore the biosynthetic origins of this useful moiety. We report here that the AHBA side chain of butirosin is transferred from the acyl carrier protein (ACP) BtrI to the parent aminoglycoside ribostamycin as a gamma-glutamylated dipeptide by the ACP:aminoglycoside acyltransferase BtrH. The protective gamma-glutamyl group is then cleaved by BtrG via an uncommon gamma-glutamyl cyclotransferase mechanism. The application of this pathway to the in vitro enzymatic production of novel AHBA-bearing aminoglycosides is explored with encouraging implications for the preparation of unnatural antibiotics via directed biosynthesis.     

The study of the changes in the thermal properties of <Emphasis Type="Italic">Labeo rohita</Emphasis> bones due to arsenic exposure

The paper presents the changes in the thermal properties of control, arsenic exposed and DMSA treated Labeo rohita bones by using thermo analytical techniques. The result shows that the mass loss due to the thermal decomposition occurs in three distinct steps due to loss of water, organic and inorganic materials. The arsenic exposed bones present a different thermal behaviour compared to the control bones. The residue masses are increased due to arsenic exposure, while the DMSA treatment reduces the residue mass level. These thermal characteristics can be used as a qualitative method to check the metal accumulation in samples.     

MIL-96, a porous aluminum trimesate 3D structure constructed from a hexagonal network of 18-membered rings and mu3-oxo-centered trinuclear units

A new aluminum trimesate Al12O(OH)18(H2O)3(Al2(OH)4)[btc]6.24H2O, denominated MIL-96, was synthesized under mild hydrothermal conditions (210 degrees C, 24 h) in the presence of 1,3,5-benzenetricarboxylic acid (trimesic acid or H3btc) in water. Hexagonal crystals, allowing a single-crystal XRD analysis, are grown from a mixture of trimethyl 1,3,5-benzenetricarboxylate (Me3btc), HF, and TEOS. The MIL-96 structure exhibits a three-dimensional (3D) framework containing isolated trinuclear mu3-oxo-bridged aluminum clusters and infinite chains of AlO4(OH)2 and AlO2(OH)4 octahedra forming a honeycomb lattice based on 18-membered rings. The two types of aluminum groups are connected to each other through the trimesate species, which induce corrugated chains of aluminum octahedra, linked via mu2-hydroxo bonds with the specific -cis-cis-trans- sequence. The 3D framework of MIL-96 reveals three types of cages. Two of them, centered at the special positions 0 0 0 and 2/3 1/3 1/4, have estimated pore volumes of 417 and 635 A3, respectively, and encapsulate free water molecules. The third one has a smaller pore volume and contains disordered aluminum octahedral species (Al(OH)6). The solid-state NMR characterization is consistent with crystal structure and elemental and thermal analyses. The four aluminum crystallographic sites are resolved by means of 27Al 3QMAS technique. This product is able to sorb both carbon dioxide and methane at room temperature (4.4 mmol.g(-1) for CO2 and 1.95 mmol.g(-1) for CH4 at 10 bar) and hydrogen at 77 K (1.91 wt % under 3 bar).     

Saxitoxin, a toxic marine natural product that targets a multitude of receptors

Saxitoxin (STX) was discovered early last century and can contaminate seafood and drinking water, and over time has become an invaluable research tool and an internationally regulated chemical weapon. Among natural products, toxins obtain a unique reputation from their high affinity and selectivity for their target pharmacological receptor, which for STX has long been considered to only be the voltage gated sodium channel. In recent times however, STX has been discovered to also bind to calcium and potassium channels, neuronal nitric oxide synthase, STX metabolizing enzymes and two circulatory fluid proteins, namely a transferrin-like family of proteins and a unique protein found in the blood of pufferfish.