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.     

Search for life on Mars.

A multi-user integrated suite of instruments designed to optimize the search for evidence of life on Mars is described. The package includes: -Surface inspection and surface environment analysis to identify the potential Mars landing sites, to inspect the surface geology and mineralogy, to search for visible surficial microbial macrofossils, to study the surface radiation budget and surface oxidation processes, to search for niches for extant life. -Subsurface sample acquisition by core drilling -Analysis of surface and subsurface minerals and organics to characterize the surface mineralogy, to analyse the surface and subsurface oxidants, to analyse the mineralogy of subsurface aliquots, to analyse the organics present in the subsurface aliquots (elemental and molecular composition, isotopes, chirality). -Macroscopic and microscopic inspection of subsurface aliquots to search for life's indicators (paleontological, biological, mineralogical) and to characterize the mineralogy of the subsurface aliquots. The study is led by ESA Manned Spaceflight and Microgravity Directorate.     

A phase II study of combined administration of dacarbazine and carboplatin with home therapy of recombinant interleukin-2 and interferon-α2a in patients with advanced malignant melanoma

Chemotherapy and interleukin-2 (IL-2) and/or interferon (IFN) produce objective responses in a proportion of patients with advanced malignant melanoma. The duration of response to chemotherapy is usually less than 4 months, and immunotherapy has resulted in longlasting remissions in a small number of patients with metastatic melanoma. The current study was conducted to improve the antitumor efficacy and the interactions between recombinant (r) IL-2, rIFN2a and chemotherapy. A total of 16 evaluable patients with metastatic malignant melanoma were entered into a phase-II study designed to assess the response rate and therapeutic efficacy of dacarbazine and carboplatin followed by rIL-2 and rIFN2a. Patients received 750 mg/m² dacarbazine with 400 mg/m² carboplatin each by intravenous bolus on days 1 and 22. Recombinant IL-2 and IFN2a were administered on an outpatient basis (home therapy) subcutaneously for 6 consecutive weeks: 4.8×10⁶ IU/m² rIL-2 daily, 5 days a week; 6.0×10⁶ IU/m² rIFN2a thrice weekly. There were responses in 6 of the 16 enrolled patients with an overall response rate of 37.5% (95% confidence interval: 14%–61%). All responding patients had partial responses. The median survival time of the responding patients was significantly better than that of patients with progressive and stable disease (P=0.03). The median duration of response was 11 months (range 2–24 months). Responses in lung, liver, soft tissue and lymph-node sites were noted.     

Comparison of dimethyl dioctadecyl ammonium bromide, Freund's complete adjuvant and mineral oil for induction of humoral antibodies, cellular immunity and resistance to Newcastle disease virus in chickens

Abstract Dimethyl diotadecyl ammonium bromide (DDA), a lipophilic quaternary amine, was evaluated in adult chickens for potentiation of immunological responses to subcutaneously administered inactivated Newcastle disease virus (NDV) vaccines. DDA enhanced humoral and cell-mediated immune (CMI) responses to levels which were significantly higher than those induced by the vaccine alone The haemagglutination inhibition antibody titers induced by DDA were slightly lower than those induced by mineral oil although neutralizing antibody titers seemed to be higher. DDA induced strong CMI (DTH and lymphocyte proliferation) responses, more than those induced by Freund's complete adjuvant and mineral oil. Both DDA and mineral oil induced comparable high levels of protection to challenge doses of 200 000 LD₅₀ per chicken. No toxic effects or local tissue damage were observed in any of the inoculated chickens.     

Soluble trinitrophenylated proteins and trinitrophenylated cells as specific inhibitors of target cell lysis by cytotoxic T lymphocytes.

Bovine serum albumin (BSA) substituted in 12 to 15 amino groups with 2,4,6-trinitrophenyl (Tnp-BSA) or carbobenzoxy (Cbz-BSA) or acetyl (Ac-BSA) groups was tested as inhibitor of the reaction in which anti-Tnp cytotoxic T lymphocytes (CTLs) lysed syngeneic ⁵¹Cr-labeled Tnp-modified spleen cells [concanavalin A (Con A) blasts]. Inhibition was observed with some consistency only with Tnp-BSA at extremely high concentration (50 mg/ml). To explore the significance of this observation, inhibition of anti-Tnp CTLs was also tested with Tnp-modified cells on which products of the major histocompatibility loci H-2K and H-2D were lacking or different from those on the stimulator cells used to elicit the CTLs. Only those Tnp cells with the same H-2 products as the stimulators were inhibitory, even though all the Tnp cells tested had essentially the same surface density of Tnp (ca 1 × 10⁸ groups/cell). It is concluded that effective specific inhibitors of anti-Tnp CTLs have both Tnp groups and the correct H-2 products on the same particle and that the specific inhibitory activity of soluble Tnp-BSA was probably due to its adsorption onto cells in the suspensions used to assay cytotoxicity.     

Increase in lipid fluidity of cellular membranes induced by adsorption of RNA and DNA virions.

Changes in the dynamic behavior of membrane lipids of mammalian cells induced by adsorption of animal viruses were quantitatively monitored by fluorescence polarization analysis with the aid of the fluorescent probe 1,6-diphenyl 1,3,5-hexatriene embedded in the surface membrane lipid core of intact cells. Adsorption of encephalomyocarditis, West Nile, and polyoma viruses to hamster (baby hamster kidney) and mouse (3T3) cells is accompanied by a rapid and significant increase in the degree of fluidity of membrane lipids of the infected cells. These changes in membrane fluidity, which are virus dose dependent, are inhibited by low temperature and by treatment of the cells before-hand with compounds known to block viral receptors on the cell surface. It is suggested that increase in membrane lipid fluidity, induced by the adsorption of virions, is an early event in the process of cell-virus interactions.     

Jatropham derivatives and steroidal saponins from the bulbs of Lilium hansonii.

Two new jatropham derivatives and three new steroidal saponins were isolated from the fresh bulbs of Lilium hansonii, along with previously known compounds. The structures of the new compounds were elucidated, on the basis of spectroscopic data and chemical evidence, and by comparing them with those of known compounds, as (-)-5-hydroxy-3-methyl-3-pyrrolin-2-one (jatropham) 5-O-beta-D-glucopyranosyl-(1----3)-beta-D-glucopyranoside, (2S*,4R*)-1-(3-methyl-2-oxo-3-pyrrolinyl)-4-methyl-5-oxo-2-pyrr olidinecarboxyli c acid, 26-O-beta-D-glucopyranosyl-(25R)-5 alpha-furostan-3 beta,22 zeta-diol 3-O-alpha-L-rhamnopyranosyl-(1----2)-O-[beta-D-glucopyranosyl-(1----4)]- beta-D-glucopyranoside, (25R)-5 alpha-spirostan-3 beta,12 alpha-diol 3-O-alpha-L-rhamnopyranosyl-(1----2)-O-[beta-D-glucopyranosyl-(1----4)]- beta-D-glucopyranoside and (25R)-spirost-5-en-3 beta,12 alpha-diol 3-O-alpha-L-rhamnopyranosyl-(1----2)-O-[beta-D-glucopyranosyl-(1----4)]- beta-D-glucopyranoside, respectively. The stereostructure of jatropham dimer, the plain structure of which was presented previously, was confirmed by X-ray crystallographic analysis. The inhibitory activity on cyclic AMP phosphodiesterase of the steroidal saponins was evaluated.     

Large herbivores facilitate an insect herbivore by modifying plant community composition in a temperate grassland

Large herbivores often co‐occur and share plant resources with herbivorous insects in grassland ecosystems; yet, how they interact with each other remains poorly understood. We conducted a series of field experiments to investigate whether and how large domestic herbivores (sheep; Ovis aries) may affect the abundance of a common herbivorous insect (aphid; Hyalopterus pruni) in a temperate grassland of northeast China. Our exclosure experiment showed that 3 years (2010–2012) of sheep grazing had led to 86% higher aphid abundance compared with ungrazed sites. Mechanistically, this facilitative effect was driven by grazing altering the plant community, rather than by changes in food availability and predator abundance for aphids. Sheep significantly altered plant community by reducing the abundance of unpalatable forbs for the aphids. Our small‐scale forb removal experiment revealed an “associational plant defense” by forbs which protect the grass Phragmites australis from being attacked by the aphids. However, selective grazing on forbs by sheep indirectly disrupted such associational plant defense, making P. australis more susceptible to aphids, consequentially increasing the density of aphids. These findings provide a novel mechanistic explanation for the effects of large herbivores on herbivorous insects by linking selective grazing to plant community composition and the responses of insect populations in grassland ecosystems.