Discovery of 2-Aminothiazoles as Potent Antiprion Compounds

Prion diseases are fatal, untreatable neurodegenerative diseases caused by the accumulation of the misfolded, infectious isoform of the prion protein (PrP), termed PrP^Sc. In an effort to identify novel inhibitors of prion formation, we utilized a high-throughput enzyme-linked immunosorbent assay (ELISA) to evaluate PrP^Sc reduction in prion-infected neuroblastoma cell lines (ScN2a). We screened a library of ∼10,000 diverse small molecules in 96-well format and identified 121 compounds that reduced PrP^Sc levels at a concentration of 5 μM. Four chemical scaffolds were identified as potential candidates for chemical optimization based on the presence of preliminary structure-activity relationships (SAR) derived from the primary screening data. A follow-up analysis of a group of commercially available 2-aminothiazoles showed this class as generally active in ScN2a cells. Our results establish 2-aminothiazoles as promising candidates for efficacy studies of animals and validate our drug discovery platform as a viable strategy for the identification of novel lead compounds with antiprion properties.Prion diseases belong to a class of neurodegenerative, protein-conformation disorders whose unifying pathological mechanism is the misprocessing and aggregation of normally benign soluble proteins. These “proteinopathies,” which include Alzheimer''s, Parkinson''s, and Huntington''s diseases, as well as the frontotemporal dementias—including Pick''s disease—and amyotrophic lateral sclerosis (ALS), are uniformly fatal after a period of neurodegeneration, characterized clinically by dementia and motor dysfunction (20). Prion diseases, which include Creutzfeldt-Jakob disease (CJD) in humans, scrapie in sheep, and bovine spongiform encephalopathy, are characterized by the formation of “spongiform” vacuolation of the brain (13). Disease onset is caused by the accumulation of a β-sheet-rich, infectious isoform of the prion protein, termed PrP^Sc (1, 16, 19, 20), which is formed from the α-helix-rich cellular prion protein, termed PrP^C. This conversion can occur spontaneously or be induced by the presence of a number of different autosomally dominant mutations of the PrP gene (8, 21). Alternatively, prion disease can result from exogenous exposure to PrP^Sc (20). The infectious nature of prions results from the ability of PrP^Sc to induce its own production by stimulating the alternative folding of PrP^C (18). Although PrP^Sc formation has been demonstrated to be the primary pathogenic event in prion disease, the precise mechanism that features in its formation and the ensuing neurodegeneration remains largely unknown.Despite the lack of a detailed understanding of the cellular mechanism of prion propagation, numerous studies have been directed toward development of therapeutics targeting prions. Screenings utilizing prion-infected cell lines have identified a number of compounds that reduce the level of PrP^Sc in culture. These include pentosan polysulfate (PPS), dextran sulfate (DS), HPA-23, Congo red, suramin, dendritic polyamines, and quinacrine, among others; for a comprehensive review, see reference 22. However, none of these have been shown to be effective against a broad range of prion strains in animal models when administered after clinical signs manifest, and none have been shown to modify the disease course in human clinical studies (22).The current array of antiprion compounds has been discovered mostly by ad hoc, low-throughput screening of small sets of known bioactive compounds. Most antiprion compounds that are active in prion-infected cell lines have failed in vivo, which highlights the need for a sustained, high-throughput drug discovery effort. Such studies need to rapidly screen large libraries of new chemical entities in vitro, analyze the pharmacokinetic and pharmacodynamic properties of the primary hits in vivo, and optimize the chemical properties of lead compounds. In two semi-high-throughput screenings for antiprion compounds, an analysis of ∼2,000-member compound libraries of known drugs and natural products identified sets of 17 and 8 active compounds (10). None of these have been reported to be effective in vivo.In the present study, we assessed the antiprion activity of ∼10,000 compounds encompassing a diverse set of chemical entities and identified a set of 121 compounds that induce the clearance of PrP^Sc. Subsequent analysis of a number of compounds with the 2-aminothiazole scaffold informed the structure-activity relationship (SAR) of this lead class.     

Iterative Structure-Based Peptide-Like Inhibitor Design against the Botulinum Neurotoxin Serotype A

The botulinum neurotoxin serotype A light chain (BoNT/A LC) protease is the catalytic component responsible for the neuroparalysis that is characteristic of the disease state botulism. Three related peptide-like molecules (PLMs) were designed using previous information from co-crystal structures, synthesized, and assayed for in vitro inhibition against BoNT/A LC. Our results indicate these PLMS are competitive inhibitors of the BoNT/A LC protease and their K_i values are in the nM-range. A co-crystal structure for one of these inhibitors was determined and reveals that the PLM, in accord with the goals of our design strategy, simultaneously involves both ionic interactions via its P1 residue and hydrophobic contacts by means of an aromatic group in the P2′ position. The PLM adopts a helical conformation similar to previously determined co-crystal structures of PLMs, although there are also major differences to these other structures such as contacts with specific BoNT/A LC residues. Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors.     

Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy

The noninvasive character of NMR spectroscopy, combined with the sensitivity of the chemical shift, makes it ideally suited to investigate the conformation, binding events and dynamics of macromolecules inside living cells. These 'in-cell NMR' experiments involve labeling the macromolecule of interest with a nonradioactive but NMR-active isotope (15N or 13C). Cellular samples are prepared either by selectively overexpressing the protein in suitable cells (e.g., bacterial cells grown on isotopically labeled media), or by injecting isotopically labeled proteins directly into either cells or cell extracts. Here we provide detailed protocols for in-cell NMR experiments in the prokaryotic organism Escherichia coli, as well as eukaryotic cells and extracts employing Xenopus laevis oocytes or egg extracts. In-cell NMR samples with proteins overexpressed in E. coli can be produced within 13-14 h. Preparing Xenopus oocyte samples for in-cell NMR experiments takes 6-14 h depending on the oocyte preparation scheme and the injection method used.     

Characterization of a G protein-coupled guanylyl cyclase-B receptor from bovine tracheal smooth muscle

A G protein-coupled natriuretic peptide-guanylyl cyclase receptor-B (NPR-B) located in plasma membranes from bovine tracheal smooth muscle shows complex kinetics and regulation. NPR-B was activated by natriuretic peptides (CNP-53 > ANP-28) at the ligand extracellular domain, stimulated by Gq-protein activators, such as mastoparan, and inhibited by Gi-sensitive chloride, interacting at the juxtamembrane domain. The kinase homology domain was evaluated by the ATP inhibition of Mn2+-activated NPR-B, which was partially reversed by mastoparan. The catalytic domain was studied by kinetics of Mn2+/Mg2+ and GTP, and the catalytic effect with GTP analogues with modifications of the /gamma phosphates and ribose moieties. Most NPR-B biochemical properties remained after detergent solubilization but the mastoparan activation and chloride inhibition of NPR-B disappeared. Our results indicate that NPR-B is a highly regulated nano-machinery with domains acting at cross-talk points with other signal transducing cascades initiated by G protein-coupled receptors and affected by intracellular ligands such as chloride, Mn2+, Mg2+, ATP, and GTP.     

Hotspots of (sub)alpine plants in the Irano-Anatolian global biodiversity hotspot are insufficiently protected

Aim

The mountainous regions in SW Asia harbour a high number of endemic species, many of which are restricted to the high-elevation zone. The (sub)alpine habitats of the region are under particular threat due to global change, but their biodiversity hotspots and conservation status have not been investigated so far.

Location

Subalpine-alpine habitats of SW Asia.

Methods

Distribution data of all (sub)alpine vascular plant species of the region were compiled, resulting in 19,680 localities from 1672 (sub)alpine species, the majority of them being restricted to the region (76%). Six quantitative indices of species diversity were used on the basis of 0.5° × 0.5° grid cells to identify (sub)alpine hotspots. Hotspots whose surface area in the (sub)alpine zone was covered by nature reserves maximally by 10% were defined as conservation gaps.

Results

A high proportion (80%) of the endemic species of the study area is range-restricted and narrowly distributed. The results of all six indices were highly correlated. Using the top 5%, 10% and 20% richest cells supported by any index, 32, 53 and 98 cells, respectively, were identified as Hotspots. Almost 60% of these Hotspots at all three levels were identified as unprotected (i.e. constituted Conservation Gaps). Generally, only 22%, 18% and 16%, respectively, of the alpine surface area of the identified Hotspots were covered by nature reserves for the top 5%, 10% and 20% richest cells, respectively.

Main conclusions

Although the rate of protection in (sub)alpine Hotspots exceeds that of the entire region it is still insufficient, because these Hotspots are much richer in endemic and in range-restricted species, but at the same time are under high pressure of global change. Therefore, the establishment of new nature reserves with high conservation efficiency in (sub)alpine habitats with a particular focus on the identified Hotspots is strongly recommended.     

The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils

Dinophytes are widely distributed in marine- and fresh-waters, but have yet to be conclusively documented in terrestrial environments. Here, we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neotropical rainforest soils. Using a phylogenetic placement approach with a reference alignment and tree, we showed that the numerous sequencing reads that were phylogenetically placed as dinophytes did not correlate with taxonomic assignment, environmental preference, nutritional mode, or dormancy. All the dinophytes in the soils are rather windblown dispersal units of aquatic species and are not biologically active residents of terrestrial environments.     

Quantification of Tumor Vessels in Glioblastoma Patients Using Time-of-Flight Angiography at 7 Tesla: A Feasibility Study

Purpose

To analyze if tumor vessels can be visualized, segmented and quantified in glioblastoma patients with time of flight (ToF) angiography at 7 Tesla and multiscale vessel enhancement filtering.

Materials and Methods

Twelve patients with newly diagnosed glioblastoma were examined with ToF angiography (TR = 15 ms, TE = 4.8 ms, flip angle = 15°, FOV = 160×210 mm², voxel size: 0.31×0.31×0.40 mm³) on a whole-body 7 T MR system. A volume of interest (VOI) was placed within the border of the contrast enhancing part on T1-weighted images of the glioblastoma and a reference VOI was placed in the non-affected contralateral white matter. Automated segmentation and quantification of vessels within the two VOIs was achieved using multiscale vessel enhancement filtering in ImageJ.

Results

Tumor vessels were clearly visible in all patients. When comparing tumor and the reference VOI, total vessel surface (45.3±13.9 mm² vs. 29.0±21.0 mm² (p<0.035)) and number of branches (3.5±1.8 vs. 1.0±0.6 (p<0.001) per cubic centimeter were significantly higher, while mean vessel branch length was significantly lower (3.8±1.5 mm vs 7.2±2.8 mm (p<0.001)) in the tumor.

Discussion

ToF angiography at 7-Tesla MRI enables characterization and quantification of the internal vascular morphology of glioblastoma and may be used for the evaluation of therapy response within future studies.     

Chromophore composition of the phycobiliprotein Cr-PC577 from the cryptophyte Hemiselmis pacifica

The cryptophyte phycocyanin Cr-PC577 from Hemiselmis pacifica is a close relative of Cr-PC612 found in Hemiselmis virescens and Hemiselmis tepida. The two biliproteins differ in that Cr-PC577 lacks the major peak at around 612 nm in the absorption spectrum. Cr-PC577 was thus purified and characterized with respect to its bilin chromophore composition. Like other cryptophyte phycobiliproteins, Cr-PC577 is an (αβ)(α′β) heterodimer with phycocyanobilin (PCB) bound to the α-subunits. While one chromophore of the β-subunit is also PCB, mass spectrometry identified an additional chromophore with a mass of 585 Da at position β-Cys-158. This mass can be attributed to either a dihydrobiliverdin (DHBV), mesobiliverdin (MBV), or bilin584 chromophore. The doubly linked bilin at position β-Cys-50 and β-Cys-61 could not be identified unequivocally but shares spectral features with DHBV. We found that Cr-PC577 possesses a novel chromophore composition with at least two different chromophores bound to the β-subunit. Overall, our data contribute to a better understanding of cryptophyte phycobiliproteins and furthermore raise the question on the biosynthetic pathway of cryptophyte chromophores.