Taba: A Tool to Analyze the Binding Affinity

Evaluation of ligand-binding affinity using the atomic coordinates of a protein-ligand complex is a challenge from the computational point of view. The availability of crystallographic structures of complexes with binding affinity data opens the possibility to create machine-learning models targeted to a specific protein system. Here, we describe a new methodology that combines a mass-spring system approach with supervised machine-learning techniques to predict the binding affinity of protein-ligand complexes. The combination of these techniques allows exploring the scoring function space, generating a model targeted to a protein system of interest. The new model shows superior predictive performance when compared with classical scoring functions implemented in the programs Molegro Virtual Docker, AutoDock4, and AutoDock Vina. We implemented this methodology in a new program named Taba. Taba is implemented in Python and available to download under the GNU license at https://github.com/azevedolab/taba . © 2019 Wiley Periodicals, Inc.     

Characterization of the Zwitterionic Intermediate in 1,1‐Carboboration of Alkynes

The reaction of a Lewis acidic borane with an alkyne is a key step in a diverse range of main group transformations. Alkyne 1,1‐carboboration, the Wrackmeyer reaction, is an archetypal transformation of this kind. 1,1‐Carboboration has been proposed to proceed through a zwitterionic intermediate. We report the isolation and spectroscopic, structural and computational characterization of the zwitterionic intermediates generated by reaction of B(C₆F₅)₃ with alkynes. The stepwise reactivity of the zwitterion provides new mechanistic insight for 1,1‐carboboration and wider B(C₆F₅)₃ catalysis. Making use of intramolecular stabilization by a ferrocene substituent, we have characterized the zwitterionic intermediate in the solid state and diverted reactivity towards alkyne cyclotrimerization.     

Evaluation of the cytotoxicity on breast cancer cell of extracts and compounds isolated from Hyptis pectinata (L.) poit

Abstract

Hyptis pectinata is a herb popularly used in Brazil for the treatment of inflammations, pain, bacterial infections and cancer. In the present study, inflorescences (MPIn), leaves (MPL), branches (MPB), root (MPR) extracts and three compounds isolated from MPIn were assayed against breast tumor cell lines. The structures of the three compounds (pectinolide J, hyptolide and pectinolide E) were determined by means of spectroscopic analysis. Pectinolide J was isolated for the first time. The MPIn, MPL and MPR exhibited specific antiproliferative activity on tumor cell lines when compared to normal cell lines with IC₅₀ of 52.01?±?0.64, 45.91?±?0.02?μg/mL and 82.84?±?0.03?μg/mL, respectively. Although the isolated substances did not present good antiproliferative activity, when the three were associated, a greater biological effect was observed, suggesting a synergistic effect. Hyptolide (5.6?±?0.4?μg/mL) showed IC₅₀ sufficiently low to be considered as a drug prototype.     

Elemental Chemometrics as Tools to Depict Stalked Barnacle (Pollicipes pollicipes) Harvest Locations and Food Safety

The stalked barnacle Pollicipes pollicipes is an abundant species on the very exposed rocky shore habitats of the Spanish and Portuguese coasts, constituting also an important economical resource, as a seafood item with high commercial value. Twenty-four elements were measured by untargeted total reflection X-ray fluorescence spectroscopy (TXRF) in the edible peduncle of stalked barnacles sampled in six sites along the Portuguese western coast, comprising a total of 90 individuals. The elemental profile of 90 individuals originated from several geographical sites (N = 15 per site), were analysed using several chemometric multivariate approaches (variable in importance partial least square discriminant analysis (VIP-PLS-DA), stepwise linear discriminant analysis (S-LDA), linear discriminant analysis (LDA), random forests (RF) and canonical analysis of principal components (CAP)), to evaluate the ability of each approach to trace the geographical origin of the animals collected. As a suspension feeder, this species introduces a high degree of background noise, leading to a comparatively lower classification of the chemometric approaches based on the complete elemental profile of the peduncle (canonical analysis of principal components and linear discriminant analysis). The application of variable selection approaches such as the VIP-PLS-DA and S-LDA significantly increased the classification accuracy (77.8% and 84.4%, respectively) of the samples according to their harvesting area, while reducing the number of elements needed for this classification, and thus the background noise. Moreover, the selected elements are similar to those selected by other random and non-random approaches, reinforcing the reliability of this selection. This untargeted analytical procedure also allowed to depict the degree of risk, in terms of human consumption of these animals, highlighting the geographical areas where these delicacies presented lower values for critical elements compared to the standard thresholds for human consumption.     

Mechanochemistry in Portugal—A Step towards Sustainable Chemical Synthesis

In Portugal, publications with mechanochemical methods date back to 2009, with the report on mechanochemical strategies for the synthesis of metallopharmaceuticals. Since then, mechanochemical applications have grown in Portugal, spanning several fields, mainly crystal engineering and supramolecular chemistry, catalysis, and organic and inorganic chemistry. The area with the most increased development is the synthesis of multicomponent crystal forms, with several groups synthesizing solvates, salts, and cocrystals in which the main objective was to improve physical properties of the active pharmaceutical ingredients. Recently, non-crystalline materials, such as ionic liquids and amorphous solid dispersions, have also been studied using mechanochemical methods. An area that is in expansion is the use of mechanochemical synthesis of bioinspired metal-organic frameworks with an emphasis in antibiotic coordination frameworks. The use of mechanochemistry for catalysis and organic and inorganic synthesis has also grown due to the synthetic advantages, ease of synthesis, scalability, sustainability, and, in the majority of cases, the superior properties of the synthesized materials. It can be easily concluded that mechanochemistry is expanding in Portugal in diverse research areas.     

K-line X-ray fluorescence from highly charged iron ions under dense astrophysical plasma conditions

In the present work, we report an investigation of plasma environment effects on the atomic parameters associated with the K-vacancy states in highly charged iron ions within the astrophysical context of accretion disks around black holes. More particularly, the sensitivity of K-line X-ray fluorescence parameters (wavelengths, radiative transition probabilities, and Auger rates) in Fe XVII–Fe XXV ions has been estimated for plasma conditions characterized by an electron temperature ranging from 10⁵ to 10⁷ K and an electron density ranging from 10¹⁸ to 10²² cm⁻³. In order to do this, relativistic multiconfiguration Dirac-Fock atomic structure calculations have been carried out by considering a time averaged Debye-Hückel potential for both the electron–nucleus and electron–electron interactions.     

Evaluation of the antiviral and antimicrobial activities of triterpenes isolated from Euphorbia segetalis

A phytochemical reinvestigation of the whole plant of Euphorbia segetalis yielded five tetracyclic triterpenes: 3beta-hydroxy-cycloart-25-en-24-one (1), cycloart-25-ene-3beta,24-diol (2), cycloart-23-ene-3beta,25-diol (3), lanosta-7,9(11),24-trien-3beta-ol (4) and lanosta-7,9(11),24(31)-trien-3beta-ol (5). beta-acetoxy-cycloart-25-en-24-one (1a) and glutinol (6), lupenone (7), dammaranodienol (9), cycloartenol acetate (10), 24-methylenecycloartanol acetate (11) and beta-sitosterol (12), isolated previously, were evaluated for their antiviral activities against Herpes simplex virus (HSV) and African swine fever virus (ASFV). Lupenone exhibited strong viral plaque inhibitory effect against HSV-1 and HSV-2. The in vitro antifungal and antibacterial activities of la, cycloart-23-ene-3beta,25-diol, 3-acetate (3a) and 6-12 were also investigated.     

Diastereo-controlled Diels–Alder cycloadditions of erythrose benzylidene-acetal 1,3-butadienes by 4-substituted-1,2,4-triazoline-3,5-dione: Evidence for the stereoelectronic effects on the dienes

Erythrose benzylidene-acetal 1,3-butadienes are studied as partners in Diels–Alder cycloadditions. A high diastereofacial improvement is found in cases where both the alcohol function is protected and a π–π interaction between the diene and dienophile is possible. Several competing factors have been studied independently in order to explain its influence on the selectivity of the cycloadditions.     

Precision of a plutonium analytical method using solvent extraction and spectrophotometry

We investigated the plutonium assay method that uses the plutonyl trinitrate tetrapropyl-ammonium ion-pair solvent extraction with spectrophotometry of the extract as a candidate method capable of providing robustness and precision. To identify and assess the effect of factors on the precision, we looked at sampling techniques, silver oxide oxidation conditions extraction time, extract stability, and temperature dependence of the extract analytical peak height and position. We obtained a precision of 0.12%.     

Improved formal total synthesis of tetrahydrometinoxocrinine

An improved, isomer-free synthesis of Tetrahydrometinoxocrinine ($\text{1}$) is described.