PREDICT modeling and in-silico screening for G-protein coupled receptors

G-protein coupled receptors (GPCRs) are a major group of drug targets for which only one x-ray structure is known (the nondrugable rhodopsin), limiting the application of structure-based drug discovery to GPCRs. In this paper we present the details of PREDICT, a new algorithmic approach for modeling the 3D structure of GPCRs without relying on homology to rhodopsin. PREDICT, which focuses on the transmembrane domain of GPCRs, starts from the primary sequence of the receptor, simultaneously optimizing multiple 'decoy' conformations of the protein in order to find its most stable structure, culminating in a virtual receptor-ligand complex. In this paper we present a comprehensive analysis of three PREDICT models for the dopamine D2, neurokinin NK1, and neuropeptide Y Y1 receptors. A shorter discussion of the CCR3 receptor model is also included. All models were found to be in good agreement with a large body of experimental data. The quality of the PREDICT models, at least for drug discovery purposes, was evaluated by their successful utilization in in-silico screening. Virtual screening using all three PREDICT models yielded enrichment factors 9-fold to 44-fold better than random screening. Namely, the PREDICT models can be used to identify active small-molecule ligands embedded in large compound libraries with an efficiency comparable to that obtained using crystal structures for non-GPCR targets.     

Rapid systemic signaling during abiotic and biotic stresses: is the ROS wave master of all trades?

Rapidly communicating the perception of an abiotic stress event, wounding or pathogen infection, from its initial site of occurrence to the entire plant, i.e. rapid systemic signaling, is essential for successful plant acclimation and defense. Recent studies highlighted an important role for several rapid whole‐plant systemic signals in mediating plant acclimation and defense during different abiotic and biotic stresses. These include calcium, reactive oxygen species (ROS), hydraulic and electric waves. Although the role of some of these signals in inducing and coordinating whole‐plant systemic responses was demonstrated, many questions related to their mode of action, routes of propagation and integration remain unanswered. In addition, it is unclear how these signals convey specificity to the systemic response, and how are they integrated under conditions of stress combination. Here we highlight many of these questions, as well as provide a proposed model for systemic signal integration, focusing on the ROS wave.     

Use of In Vitro and Predictive In Silico Models to Study the Inhibition of Cytochrome P4503A by Stilbenes

CYP3A4 is recognized as the main enzyme involved in the metabolism of drugs and xenobiotics in the human body and its inhibition may lead to undesirable consequences. Stilbenes, including resveratrol, belong to a group of dietary health-promoting compounds that also act as inhibitors of CYP3A4. The aim of this study was to examine the use of computer modeling of enzyme-ligand interactions to analyze and predict the inhibition of structurally related compounds. To this end, an aldehyde group was attached to resveratrol and the interactions of CYP3A4 with resveratrol, its aldehyde analogue (RA) and a known synthetic inhibitor were studied and compared in two biological models. Specifically, the metabolism of testosterone was examined in a human intestine cell line (Caco-2/TC7) and in rat liver microsomes (RLM). The results demonstrated a weak inhibitory effect of RA on CYP3A4, as compared to resveratrol itself, in both biological models. Human CYP3A4 was more susceptible to inhibition than the commonly used model isozyme from rat. Modeling of the binding site of CYP3A4 revealed a combination of three types of interactions: hydrophobic interactions, electrostatic interactions and hydrogen bonds. A docking simulation revealed that the RA lacked an important binding feature, as compared to resveratrol, and that that difference may be responsible for its lower level of affinity for CYP3A4. Software analysis of binding affinity may serve as a predictive tool for designing new therapeutic compounds in terms of inhibition of CYP3A4 and help to reveal the biochemical nature of the interactions of dietary compounds, herbal compounds and drugs whose metabolism is mediated by this enzyme.     

Aboveground plant-to-plant electrical signaling mediates network acquired acclimation

Systemic acquired acclimation and wound signaling require the transmission of electrical, calcium, and reactive oxygen species (ROS) signals between local and systemic tissues of the same plant. However, whether such signals can be transmitted between two different plants is largely unknown. Here, we reveal a new type of plant-to-plant aboveground direct communication involving electrical signaling detected at the surface of leaves, ROS, and photosystem networks. A foliar electrical signal induced by wounding or high light stress applied to a single dandelion leaf can be transmitted to a neighboring plant that is in direct contact with the stimulated plant, resulting in systemic photosynthetic, oxidative, molecular, and physiological changes in both plants. Furthermore, similar aboveground changes can be induced in a network of plants serially connected via touch. Such signals can also induce responses even if the neighboring plant is from a different plant species. Our study demonstrates that electrical signals can function as a communication link between transmitter and receiver plants that are organized as a network (community) of plants. This process can be described as network-acquired acclimation.

A new type of plant-to-plant direct communication involving electrical signaling, reactive oxygen species, and photosystem networks is revealed.

In a Nutshell Background: An injured leaf (e.g. by insect herbivory or excess light) generates electric signals (ES) that spread to tissues, leaves, and organs of the entire plant. ES are mediated by changes in the activity of ion channels and are accompanied by waves of reactive oxygen species (ROS) and nonphotochemical quenching (NPQ). These waves are interdependent and propagate systemically throughout the plant. This process is essential for priming specific changes in gene expression and plant acclimation (e.g. cellular light memory). As a result, the entire plant enters a state of systemic acquired acclimation (SAA). Question: Could ES, ROS, and NPQ waves spread from an injured plant to neighboring plants, if their leaves touch? Until now, only indirect signaling routes like underground ES mediated by mycorrhizal networks between roots of different plants, or aboveground plant volatiles, were found to connect different plants. Findings: Under humid conditions, an injured plant can directly communicate a danger signal to other plants that touch it within a community of plants, like a meadow of dandelions. ES and ROS waves serve as plant-to-plant signals propagating on and in the leaf with a velocity of several millimeters per second or centimeters per minute, respectively. These signals can induce changes in NPQ, chloroplast retrograde signaling, gene expression, phytohormones, ROS signaling, and acclimation responses, in neighboring plants. Most of these complex communication responses can also be induced between two plants connected by a copper wire circuit, indicating that ES is the main player of plant-to-plant communication. We show that ES and ROS induce a new acclimation phenomenon termed “network acquired acclimation (NAA),” necessary for SAA induction within a plant community. Next steps: NAA may be considered as a new communication mechanism within plant ecosystems. However, whether NAA is a “side effect” of SAA, or confers an evolutionary advantage to plants living within the community, and to what extent can ES carry specific information and determine specific responses, are open questions.     

Sporotrichosis After Tattooing Caused by Sporothrix brasiliensis

Sporotrichosis is a subcutaneous mycosis caused by pathogenic species of the genus Sporothrix. Since 1998, the number of cases of sporotrichosis due to Sporothrix brasiliensis has grown significantly in Rio de Janeiro, Brazil. Nearly all cases are related to cats as the main source of fungal infection. We report two cases of sporotrichosis following tattoos, a transmission form of S. brasiliensis not yet reported. The first patient, a 22-year-old female, had cutaneous sporotrichosis, fixed form, over a tattoo in her lumbar region. The lesion appeared 12 weeks after she was tattooed. The second patient, a 27-year-old female, had a lymphocutaneous sporotrichosis over a forearm tattoo. The lesion appeared two weeks after she was tattooed. In both cases there was no history of contact with cats or other plausible source of infection. The present study highlights that other non-zoonotic forms of transmission of S. brasiliensis may occur in endemic areas.

     

Resister's logic: the anti-vaccination arguments of Alfred Russel Wallace and their role in the debates over compulsory vaccination in England, 1870-1907

In the 1880s, Alfred Russel Wallace, the celebrated co-discoverer of natural selection, launched himself into the centre of a politicised and polarised debate over the unpopular compulsory vaccination laws in England. Wallace never wavered in his belief that smallpox vaccination was useless and likely dangerous. Six years before his death, the anti-vaccinationists successfully secured a conscience clause that effectively dismantled the compulsory vaccination laws. Several other important Victorian scientists joined Wallace in the fight to repeal compulsory vaccination arguing that widely held views on the effectiveness of vaccination and evidence for immunity were inconclusive in the light of (then) contemporary standards of evidence. This article situates Wallace's anti-vaccination logic within the broader matrix of sociopolitical and cultural reform movements of the late Victorian era. Additionally it provides the first detailed analysis of his critique of vaccination science, in particular the role statistics played in his arguments. In this period, both pro-vaccinationists and anti-vaccinationists invested great efforts in collating and analysing statistical data sets that either supported or refuted the claims of vaccination's effectiveness. While each side presented 'controlled' case studies to support their assertions, without an unambiguous test to measure or demonstrate vaccination's effectiveness, the anti-vaccinationists continued to mount credible statistical critiques of vaccination science.     

Chlorpropamide and tolbutamide inhibition of adenosine 3'5' cyclic monophosphate phosphodiesterase

These sulfonylurea agents inhibit the cyclic AMP phosphodiesterase, and thereby could increase the steady state level of cyclic AMP in various tissues, depending upon the tissue concentrations achieved after oral or parental administration.