D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (1) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (2) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural data; and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand–protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy. Unlike previous blinded Challenges, we did not provide cognate receptors or receptors prepared with hydrogens and likewise did not require a specified crystal structure to be used for pose or affinity prediction in Stage 1. Given the freedom to select from over 200 crystal structures of HSP90 in the PDB, participants employed workflows that tested not only core docking and scoring technologies, but also methods for addressing water-mediated ligand–protein interactions, binding pocket flexibility, and the optimal selection of protein structures for use in docking calculations. Nearly 40 participating groups submitted over 350 prediction sets for Grand Challenge 2015. This overview describes the datasets and the organization of the challenge components, summarizes the results across all submitted predictions, and considers broad conclusions that may be drawn from this collaborative community endeavor.     

Changes in mouse Leydig cells ultrastructure and testosterone secretion after diethylcarbamazine administration

Diethylcarbamazine (DEC) has been proven to be highly effective against lymphatic filariasis, although its effect on vertebrate cells remains uncertain. Mice Leydig cells after treatment with 200mg/kg of DEC for 12 days showed numerous lipid droplets, degenerated mitochondria, residual bodies and several giant whorl-like smooth endoplasmic reticulum, some of them encircling large lipids droplets. Treatment with lower dosages showed similar alterations on Leydig cells and the morphological effects decreased directly proportional to the drug concentration. Serum testosterone levels were significantly lower only in 200 mg/kg DEC-treated group when compared to the controls. However, no significant changes were observed in the pregnancy rates and offspring number of DEC-treated male-mated female mice in any doses studied. The results obtained in the present study are consistent with the hypothesis that DEC has some effects on mice Leydig cells, although they were not sufficient enough to interfere with the rodent fertility.     

Effect of Polymer Strengtheners on the Local Environment of Biocompatible Glass as Probed by Fluorescence

Mixed silica–calcite matrices were prepared by developing a “low” temperature (sol–gel) method in presence of several biocompatible polymers, thus providing samples with adequate porosity for the flow of biological fluids and also mechanically robust. In order to analyse and characterise the sample’s microenvironments, the highly solvatochromic probe Nile red was used, which enabled the role of polymer addition upon local environmental effects in the host media to be elucidated. The polymers used were polyethylene glycol, polymethylmethacrylate and polyethylene. Each matrix was also characterized with respect to microstructure, morphology and pore size via the use of X-ray diffractometry and scanning electron microscopy. The results show that is was possible to obtain, in a controlled way, mixed silica–calcite matrices with a wide range of porosities (important if the material is to be used for scaffold or drug release applications, for example). The spectroscopic behaviour of Nile red when incorporated has confirmed the existence of distinct and specific local polarities within each type of matrix that may determine to a large extent the mechanism of interaction between these matrices and biological molecules. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Laser-Induced Fluorescence at 488 nm Excitation for Detecting Benign and Malignant Lesions in Stomach Mucosa

This work aims the detection of the histopathologic alterations of in vitro human gastric mucosa using spectral informations from laser-induced fluorescence spectroscopy (LIFS) technique with excitation at 488 nm (argon laser). A total of 108 biopsies with endoscopic diagnosis of gastritis and gastric cancer were obtained at the antral gastric region, from 35 patients with dyspeptic digestive complaints. The biopsies were collected during the endoscopic examination. On each biopsy fragment the autofluorescence spectrum was collected in two random points, through a fiber-optic catheter coupled to the excitation laser. The fluorescence emission spectra collected by the fibers were directed to the spectrograph and detected by the CCD camera. The spectra were then separated in groups (N, normal; LI, light inflammation; MI, moderated inflammation; CA, adenocarcinoma), based on the histopathology. The ratio between the emission wavelengths 550 and 600 nm was used as a diagnostic parameter. Analysis of fluorescence spectra was able to identify the normal tissue from adenocarcinoma lesions with 100% of sensibility and specificity. The ratio intensities between inflammation (light and moderated), although presented significantly statistical differences when compared to the normal mucosa, do not furnish enough sensibility and specificity for use as an identification method due to high variations. LIFS, with excitation of 488 nm, could be used in the differentiation of normal tissue and neoplasic lesions, assisting a less invasive diagnosis.     

A blind algorithm for reverberation-time estimation using subband decomposition of speech signals

An algorithm for blind estimation of reverberation time (RT) in speech signals is proposed. Analysis is restricted to the free-decaying regions of the signal, where the reverberation effect dominates, yielding a more accurate RT estimate at a reduced computational cost. A spectral decomposition is performed on the reverberant signal and partial RT estimates are determined in all signal subbands, providing more data to the statistical-analysis stage of the algorithm, which yields the final RT estimate. Algorithm performance is assessed using two distinct speech databases, achieving 91% and 97% correlation with the RTs measured by a standard nonblind method, indicating that the proposed method blindly estimates the RT in a reliable and consistent manner.     

Pionic hydrogen and deuterium

The ground-state level shifts and broadenings of the hydrogen isotopes caused by the strong interaction have been redetermined by using a high-resolution crystal spectrometer. An additional measurement of muonic hydrogen reveals properties of the de-excitation cascade of such electrically neutral exotic atoms, in particular Coulomb de-excitation, the understanding of which is essential for the analysis of the hadronic-atom data.