Simplified,interpretable graph convolutional neural networks for small molecule activity prediction

Journal of Computer-Aided Molecular Design - We here present a streamlined, explainable graph convolutional neural network (gCNN) architecture for small molecule activity prediction. We first...     

Survey of Phenolic Acids,Flavonoids and In Vitro Antioxidant Potency Between Fig Peels and Pulps: Chemical and Chemometric Approach

In the present study, chromatic coordinates, phenolic acids, flavonoids and antioxidant capacity assessed by 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonate (ABTS) and lipid peroxidation inhibition capacity (LPIC) essays and their relative IC50 were investigated in 25 fig cultivars growing in Morocco. The aims of this study were to determine (i) the variation in these compounds among light and dark-colored cultivars, (ii) their partitioning between fruit peel and pulp and (iii) to display network connections among these variables. Twelve phenolic compounds (PCs) were isolated in peel extract versus eight in pulp samples. Anthocyanins, mainly cyanidin-3,5-diglucoside and cyanidin-3-O-rutinoside, were the predominant compounds in peels, where the mean concentrations were 75.90 ± 18.76 and 77.97 ± 18.95 µg/g dw, respectively. On the other hand, (−)-epicatechin and cyanidin-3-O-rutinoside were the major compounds in the pulp extracts, where the mean values were 5.23 ± 4.03 and 9.01 ± 5.67 µg/g dw, respectively. A two-dimensional hierarchically clustered heatmap was applied to the dataset to explore correlations in the dataset and similarities between cultivars, without dimensionality reduction. Results showed that anthocyanins, particularly pelargonidin-3-O-rutinoside, cyanidin-3,5-diglucoside and cyanidin-3-O-rutinoside, were the main contributors to the peels’ free radical scavenging capacity. This capacity was particularly higher in the peel of dark-colored figs compared to the fruit pulp. The local cultivar “INRA 1301” showed the most promising phenolic profile due to its very high levels of almost all detected PCs, especially (−)-epicatechin, quercetin-3-O-rutinoside, quercetin-3-O-glucoside, cyanidine-3,5-diglucoside, cyanidine-3-O-rutinoside and pelargonidin-3-O-rutinoside (54.66, 141.08, 35.48, 494.08, 478.66, 12.56 µg/g dw, respectively). Having the darkest figs in the collection (L* = 25.72, c* = 22.09 and h° = 20.99), this cultivar has also combined promising IC50 values, which were of 19.85, 40.58 and 124.78 µg/mL for DPPH, ABTS and LPIC essays, respectively.     

Line tension at fluid membrane domain boundaries measured by micropipette aspiration

Line tension is a determinant of fluid phase domain formation kinetics and morphology in lipid bilayer membranes, which are models for biological membrane heterogeneity. We describe the first direct measurement of this line tension by micropipette aspiration. Our data are analyzed with a model that does not rely on independently measured (and composition dependent) secondary parameters, such as bending stiffness or membrane viscosities. Line tension is strongly composition dependent and decreases towards a critical consolute point in a quasiternary room temperature phase diagram.     

Liquid transport due to light scattering

Using experiments and theory, we show that light scattering by inhomogeneities in the index of refraction of a fluid can drive a large-scale flow. The experiment uses a near-critical, phase-separated liquid, which experiences large fluctuations in its index of refraction. A laser beam traversing the liquid produces a interface deformation on the scale of the experimental setup and can cause a liquid jet to form. We demonstrate that the deformation is produced by a scattering-induced flow by obtaining good agreements between the measured deformations and those calculated assuming this mechanism.     

Diagnosis of suspicious breast lesions using an empirical mathematical model for dynamic contrast-enhanced MRI

The purpose of this study was to test whether an empirical mathematical model (EMM) of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) can distinguish between benign and malignant breast lesions. A modified clinical protocol was used to improve the sampling of contrast medium uptake and washout. T(1)-weighted DCE magnetic resonance images were acquired at 1.5 T for 22 patients before and after injection of Gd-DTPA. Contrast medium concentration as a function of time was calculated over a small region of interest containing the most rapidly enhancing pixels. Then the curves were fitted with the EMM, which accurately described contrast agent uptake and washout. Results demonstrate that benign lesions had uptake (P<2.0 x 10(-5)) and washout (P<.01) rates of contrast agent significantly slower than those of malignant lesions. In addition, secondary diagnostic parameters, such as time to peak of enhancement, enhancement slope at the peak and curvature at the peak of enhancement, were derived mathematically from the EMM and expressed in terms of primary parameters. These diagnostic parameters also effectively differentiated benign from malignant lesions (P<.03). Conventional analysis of contrast medium dynamics, using a subjective classification of contrast medium kinetics in lesions as "washout," "plateau" or "persistent" (sensitivity=83%, specificity=50% and diagnostic accuracy=72%), was less effective than the EMM (sensitivity=100%, specificity=83% and diagnostic accuracy=94%) for the separation of benign and malignant lesions. In summary, the present research suggests that the EMM is a promising alternative method for evaluating DCE-MRI data with improved diagnostic accuracy.     

Zundel-Type H-Bonding in Biomolecular Ions

Using quantum chemical calculations and infrared multiphoton dissociation (IRMPD) spectroscopy in the fingerprint and X-H stretching regions, we demonstrate here that the all-Ala b ₆ fragment ion features a macrocyclic structure with C₂ symmetry. For this structure, the ionizing proton is equally shared by the Ala(1) and Ala(4) amide oxygens in a Zundel-type symmetric (X…H⁺…X) H-bond. Figure

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Enzyme Design from the Bottom Up: An Active Nickel Electrocatalyst with a Structured Peptide Outer Coordination Sphere

Catalytic, peptide‐containing metal complexes with a well‐defined peptide structure have the potential to enhance molecular catalysts through an enzyme‐like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide‐based metal complex built upon the well‐characterized hydrogen production catalyst [Ni(P^Ph₂N^Ph)₂]²⁺ (P^Ph₂N^Ph=1,3,6‐triphenyl‐1‐aza‐3,6‐diphosphacycloheptane). The incorporated peptide maintains its β‐hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide‐based metal complex (≈100,000 s^?1) is enhanced compared to the parent complex ([Ni(P^Ph₂N^APPA)₂]²⁺; ≈50,500 s^‐1). The combination of an active molecular catalyst with a structured peptide provides a scaffold that permits the incorporation of features of an enzyme‐like outer‐coordination sphere necessary to create molecular electrocatalysts with enhanced functionality.     

Efficient Screening for Ternary Molecular Ionic Cocrystals Using a Complementary Mechanosynthesis and Computational Structure Prediction Approach

The discovery of molecular ionic cocrystals (ICCs) of active pharmaceutical ingredients (APIs) widens the opportunities for optimizing the physicochemical properties of APIs whilst facilitating the delivery of multiple therapeutic agents. However, ICCs are often observed serendipitously in crystallization screens and the factors dictating their crystallization are poorly understood. We demonstrate here that mechanochemical ball milling is a versatile technique for the reproducible synthesis of ternary molecular ICCs in less than 30 min of grinding with or without solvent. Computational crystal structure prediction (CSP) calculations have been performed on ternary molecular ICCs for the first time and the observed crystal structures of all the ICCs were correctly predicted. Periodic dispersion-corrected DFT calculations revealed that all the ICCs are thermodynamically stable (mean stabilization energy=−2 kJ mol⁻¹) relative to the crystallization of a physical mixture of the binary salt and acid. The results suggest that a combined mechanosynthesis and CSP approach could be used to target the synthesis of higher-order molecular ICCs with functional properties.     

Characterization of Bioactive Compounds of Opuntia ficus-indica (L.) Mill. Seeds from Spanish Cultivars

Opuntia ficus-indica (L.) Mill. is the Cactaceae plant with the greatest economic relevance in the world. It can be used for medicinal purposes, animal nutrition, production of biofuels and phytoremediation of soils. Due to its high content of bioactive compounds, the prickly pear has antioxidant, antimicrobial and anticancer properties. The aim of this study was to determine the polyphenolic, fatty acid and amino acid profile and characterize the antioxidant capacity of seeds of seven Spanish prickly pear cultivars. A total of 21 metabolites, mainly phenolic acids and flavonols, were identified using ultraperformance liquid chromatography photodiode detector quadrupole/time-of-flight mass spectrometry (UPLC-PDA-Q/TOF-MS). Significant differences were found in the phenolic concentrations of the investigated varieties. The highest amount of phenolic compounds (266.67 mg/kg dry matter) were found in the “Nopal espinoso” variety, while the “Fresa” variety was characterized by the lowest content (34.07 mg/kg DM) of these compounds. In vitro antioxidant capacity was positively correlated with the amount of polyphenols. The amino acid composition of protein contained in prickly pear seeds was influenced by the variety. Glutamic acid was the predominant amino acid followed by arginine, aspartic acid and leucine, independent of prickly pear variety. Overall, 13 different fatty acids were identified and assessed in prickly pear seeds. The dominant fatty acid was linoleic acid, with content varying between 57.72% “Nopal ovalado” and 63.11% “Nopal espinoso”.     

High Compression‐Induced Conductivity in a Layered Cu–Br Perovskite

We show that the onset pressure for appreciable conductivity in layered copper‐halide perovskites can decrease by ca. 50 GPa upon replacement of Cl with Br. Layered Cu–Cl perovskites require pressures >50 GPa to show a conductivity of 10^?4 S cm^?1, whereas here a Cu–Br congener, (EA)₂CuBr₄ (EA=ethylammonium), exhibits conductivity as high as 2×10^?3 S cm^?1 at only 2.6 GPa, and 0.17 S cm^?1 at 59 GPa. Substitution of higher‐energy Br 4p for Cl 3p orbitals lowers the charge‐transfer band gap of the perovskite by 0.9 eV. This 1.7 eV band gap decreases to 0.3 eV at 65 GPa. High‐pressure X‐ray diffraction, optical absorption, and transport measurements, and density functional theory calculations allow us to track compression‐induced structural and electronic changes. The notable enhancement of the Br perovskite's electronic response to pressure may be attributed to more diffuse Br valence orbitals relative to Cl orbitals. This work brings the compression‐induced conductivity of Cu‐halide perovskites to more technologically accessible pressures.