Discovery and development of next generation sGC stimulators with diverse multidimensional pharmacology and broad therapeutic potential.

Nitric oxide (NO)-sensitive soluble guanylyl cyclase (sGC), an enzyme that catalyzes the conversion of guanosine-5'-triphosphate (GTP) to cyclic guanosine-3',5'-monophophate (cGMP), transduces many of the physiological effects of the gasotransmitter NO. Upon binding of NO to the prosthetic heme group of sGC, a conformational change occurs, resulting in enzymatic activation and increased production of cGMP. cGMP modulates several downstream cellular and physiological responses, including but not limited to vasodilation. Impairment of this signaling system and altered NO-cGMP homeostasis have been implicated in cardiovascular, pulmonary, renal, gastrointestinal, central nervous system, and hepatic pathologies. sGC stimulators, small molecule drugs that synergistically increase sGC enzyme activity with NO, have shown great potential to treat a variety of diseases via modulation of NO-sGC-cGMP signaling. Here, we give an overview of novel, orally available sGC stimulators that Ironwood Pharmaceuticals is developing. We outline the non-clinical and clinical studies, highlighting pharmacological and pharmacokinetic (PK) profiles, including pharmacodynamic (PD) effects, and efficacy in a variety of disease models.

Differential effects of air conditioning type on residential endotoxin levels in a semi-arid climate.

Residential endotoxin exposure is associated with protective and pathogenic health outcomes. Evaporative coolers, an energy-efficient type of air conditioner used in dry climates, are a potential source of indoor endotoxins; however, this association is largely unstudied. We collected settled dust biannually from four locations in homes with evaporative coolers (n=18) and central air conditioners (n=22) in Utah County, Utah (USA), during winter (Jan-Apr) and summer (Aug-Sept), 2014. Dust samples (n=281) were analyzed by the Limulus amebocyte lysate test. Housing factors were measured by survey, and indoor temperature and relative humidity measures were collected during both seasons. Endotoxin concentrations (EU/mg) were significantly higher in homes with evaporative coolers from mattress and bedroom floor samples during both seasons. Endotoxin surface loads (EU/m2 ) were significantly higher in homes with evaporative coolers from mattress and bedroom floor samples during both seasons and in upholstered furniture during winter. For the nine significant season-by-location comparisons, EU/mg and EU/m2 were approximately three to six times greater in homes using evaporative coolers. A plausible explanation for these findings is that evaporative coolers serve as a reservoir and distribution system for Gram-negative bacteria or their cell wall components in homes.

Evolutionary relationships among G protein-coupled receptors using a clustered database approach.

Guanine nucleotide-binding protein-coupled receptors (GPCRs) comprise large and diverse gene families in fungi, plants, and the animal kingdom. GPCRs appear to share a common structure with 7 transmembrane segments, but sequence similarity is minimal among the most distant GPCRs. To reevaluate the question of evolutionary relationships among the disparate GPCR families, this study takes advantage of the dramatically increased number of cloned GPCRs. Sequences were selected from the National Center for Biotechnology Information (NCBI) nonredundant peptide database using iterative BLAST (Basic Local Alignment Search Tool) searches to yield a database of approximately 1700 GPCRs and unrelated membrane proteins as controls, divided into 34 distinct clusters. For each cluster, separate position-specific matrices were established to optimize sequence comparisons among GPCRs. This approach resulted in significant alignments between distant GPCR families, including receptors for the biogenic amine/peptide, VIP/secretin, cAMP, STE3/MAP3 fungal pheromones, latrophilin, developmental receptors frizzled and smoothened, as well as the more distant metabotrobic glutamate receptors, the STE2/MAM2 fungal pheromone receptors, and GPR1, a fungal glucose receptor. On the other hand, alignment scores between these recognized GPCR clades with p40 (putative GPCR) and pm1 (putative GPCR), as well as bacteriorhodopsins, failed to support a finding of homology. This study provides a refined view of GPCR ancestry and serves as a reference database with hyperlinks to other sources. Moreover, it may facilitate database annotation and the assignment of orphan receptors to GPCR families.

Molecular modeling of G-protein coupled receptor kinase 2: docking and biochemical evaluation of inhibitors.

G-protein coupled receptor kinase 2 (GRK2) regulates the activity of many receptors. Because potent inhibitors of GRK2 are thus far limited to polyanionic compounds like heparin, we searched for new inhibitors with the aid of a molecular model of GRK2. We used the available crystal structure of cAMP dependent protein kinase (cAPK) as a template to construct a 3D homology model of GRK2. Known cAPK and GRK2 inhibitors were docked into the active sites of GRK2 and cAPK using DOCK v3.5. H8 docked into the hydrophobic pocket of the adenosine 5'-triphosphate (ATP) binding site of cAPK, consistent with its known competitive cAPK inhibition relative to ATP. Similarly, 3 of 4 known GRK2 inhibitors docked into the ATP binding pocket of GRK2 with good scores. Screening the Fine Chemicals Directory (FCD, containing the 3D structures of 13,000 compounds) for docking into the active sites of GRK2 identified H8 and the known GRK2 inhibitor trifluoperazine as candidates. Whereas H8 indeed inhibited light-dependent phosphorylation of rhodopsin by GRK2, but with low potency, 3 additional FCD compounds with promising GRK2 scores failed to inhibit GRK2. This result demonstrates limitations of the GRK2 model in predicting activity among diverse chemical structures. Docking suramin, an inhibitor of protein kinase C (not present in FCD) yielded a good fit into the ATP binding site of GRK2 over cAPK. Suramin did inhibit GRK2 with IC50 32 microM (pA26.39 for competitive inhibition of ATP). Suramin congeners with fewer sulfonic acid residues (NF062, NF503 [IC50 14 microM]) or representing half of the suramin molecule (NF520) also inhibited GRK2 as predicted by docking. In conclusion, suramin and analogues are lead compounds in the development of more potent and selective inhibitors of GRK2.

Human proton/oligopeptide transporter (POT) genes: identification of putative human genes using bioinformatics.

The proton-dependent oligopeptide transporters (POT) gene family currently consists of approximately 70 cloned cDNAs derived from diverse organisms. In mammals, two genes encoding peptide transporters, PepT1 and PepT2 have been cloned in several species including humans, in addition to a rat histidine/peptide transporter (rPHT1). Because the Candida elegans genome contains five putative POT genes, we searched the available protein and nucleic acid databases for additional mammalian/human POT genes, using iterative BLAST runs and the human expressed sequence tags (EST) database. The apparent human orthologue of rPHT1 (expression largely confined to rat brain and retina) was represented by numerous ESTs originating from many tissues. Assembly of these ESTs resulted in a contiguous sequence covering approximately 95% of the suspected coding region. The contig sequences and analyses revealed the presence of several possible splice variants of hPHT1. A second closely related human EST-contig displayed high identity to a recently cloned mouse cDNA encoding cyclic adenosine monophosphate (cAMP)-inducible 1 protein (gi:4580995). This contig served to identify a PAC clone containing deduced exons and introns of the likely human orthologue (termed hPHT2). Northern analyses with EST clones indicated that hPHT1 is primarily expressed in skeletal muscle and spleen, whereas hPHT2 is found in spleen, placenta, lung, leukocytes, and heart. These results suggest considerable complexity of the human POT gene family, with relevance to the absorption and distribution of cephalosporins and other peptoid drugs.

The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors.

Located between the inner and outer membranes of Gram-negative bacteria, periplasmic binding proteins (PBPs) scavenge or sense diverse nutrients in the environment by coupling to transporters or chemotaxis receptors in the inner membrane. Their three-dimensional structures have been deduced in atomic detail with the use of X-ray crystallography, both in the free and liganded state. PBPs consist of two large lobes that close around the bound ligand, resembling a Venus flytrap. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. Many of these receptors are promising drug targets. On the basis of homology to PBPs and a recently resolved crystal structure of the extracellular binding domain of a glutamate receptor ion channel, it is possible to construct three-dimensional models of their ligand binding domains. Together with the extensive information available on the mechanism of ligand binding to PBPs, such models can serve as a guide in drug discovery.

Sequence alignments of the H(+)-dependent oligopeptide transporter family PTR: inferences on structure and function of the intestinal PET1 transporter.

PURPOSE: To study the structure and function of the intestinal H+/ peptide transporter PET1, we compared its amino acid sequence with those of related transporters belonging to the oligopeptide transporter family PTR, and with more distant transporter families. METHODS: We have developed a new approach to the sequence analysis of proteins with multiple transmembrane domains (TMDs) which takes into account the repeated TMD-loop topology. In addition to conventional analyses of the entire sequence, each TMD and its adjacent loop residues (= TMD segments) were analyzed separately as independent structural units. In combination with hydropathy analysis, this approach reveals any changes in the order of the TMD segments in the primary structure and permits TMD alignments among divergent structures even if rearrangements of the order of TMD segments have occurred in the course of evolution. RESULTS: Alignments of TMD segments indicate that the TMD order in PTR transporters may have changed in the process of evolution. Consideration of such changes permits the alignment of homologous TMD segments from PTR transporters belonging to distant akaryotic and eukaryotic phyla. Multiple alignments of TMDs reveal several highly conserved regions that may play a role in transporter function. In comparing the PTR transporters with other transporter gene families, alignment scores using the entire primary structure are too low to support a finding of probable homology. However, statistically significant alignments were observed among individual TMD segments if one disregards the order in which they occur in the primary structure. CONCLUSIONS: Our results support the hypothesis that the PTR transporters may have evolved by rearrangement, duplication, or insertions and deletions of TMD segments as independent modules. This modular structure suggests new alignment strategies for determining functional domains and testing relationship among distant transporter families.

Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsins with the yeast sequence YRO2.

PURPOSE: Searching the existing databases for homologous sequences is essential to understanding a protein's structure and function. For a query sequence, its nearest neighbors can be identified by BLAST (basic local alignment search tool). However, a single query sequence is sufficient to define the entire neighborhood of related sequences, and multiple BLAST queries are needed. We describe here a program which permits automated and iterative BLAST analysis of an entire neighborhood of sequences and apply this to search for homologs of the bacteriorhodopsins outside the archaea phylum. METHODS: We have developed a Java program, 'Iterative Neighborhood Cluster Analysis' (INCA), which performs iterative BLAST searches, beginning with a single starter sequence, and proceeding with any other sequence achieving a predefined minimum alignment score. This results in a cluster of sequences where each sequence is related to at least one other sequence by the cutoff score, additional lists of more distantly related sequences for each member of cluster. RESULTS: Bacteriorhodopsins had not been previously aligned with any other protein family with scores indicative of probable homology. Using INCA, we identified a probable homolog in yeast, YRO2_YEAST, also containing seven putative transmembrane domains. A finding of probable homology was supported by additional alignment strategies. CONCLUSIONS: INCA is a useful tool to assess complete protein neighborhoods. With an increasing database, INCA can serve to detect the emergence of evolutionary links between even the most distantly related protein families. Identifying a homolog of the bacteriorhodopsins in yeast illustrates this approach but at the same time highlights the vast evolutionary distances between polytopic membrane proteins, such as the bacteriorhodopsins.

[Animal experiments for testing the behavior of compacted bone sections using compression osteosynthesis after hyperthermic denaturation]. / Tierexperimentelle Untersuchungen zum Liegeverhalten kompakter Osteoresektate unter Kompressionsosteosynthese nach hyperthermischer Denaturierung.

In animal experiments on domestic pigs the behaviour of hyperthermically denatured autogenic compact bone grafts after orthotopic replantation was investigated histologically. It was shown that the inductive osteogenetic celldifferentiation of the lair tissue caused by the autogenetic osteoimplantation depends on the location relationship of the replanted bone grafts to the lair bone tissue. This differentiation had progressed after 14 and 21 days further in the upper indifference area than in the contact and fissure healing area.

Cytophotometric and interference microscopic investigations in carcinomas of the oral cavity.

The DNA content and the nuclear dry mass of 18 keratinized squamous cell carcinomas and their metastases, of one adamantinoma recurrence and two adenoid cystic carcinomas of the oral cavity were determined in comparison to the normal buccal mucosa using Feulgen scanning cytophotometry and interference microscopy. The squamous cell carcinomas could be classified into five groups based on their DNA distribution pattern. The nuclear dry mass and its variation were found to be different from the normal mucosal epithelial cells in all cases. No differences could be found between diploid cells and cells of a higher degree of ploidy. Therefore the relation of nuclear dry mass and DNA content appeared to be lower in cells of higher DNA ploidy. This fact is discussed in relation to the underlying molecular biological processes. This leads to the conclusion that the increase of the nuclear dry mass (mainly protein) precedes the increase of the DNA content. The combined measurement of DNA content and nuclear dry mass allows a better characterization of malignancy than each of the nuclear components measured alone. The difference of nuclear dry mass between malignant cells and normal mucosal epithelial cells is more sensitive than the deviation of the DNA content owing to the fact that malignant tumours with normal DNA content exist.

Treatment of alcohol-related liver disease with thioctic acid: a six month randomised double-blind trial.

A randomised double-blind trial of thioctic acid (alpha-lipoic acid), 300 mg/day versus placebo was carried out in 40 patients with pre-cirrhotic alcohol-related liver disease over a six month period. Twenty patients received the active drug and 20 placebo. Twenty-two of the 40 patients (55%) abstained from alcohol and showed significant improvements (p less than 0.01) in mean values for serum aspartate transaminase, serum glutamyl transpeptidase, and mean corpuscular volume. Seventeen of the 22 (77%) showed overall histological improvement on liver biopsy. The remaining 18 patients (45%) continued to drink but significantly reduced their mean daily alcohol intake (p less than 0.001). No significant changes occurred in their laboratory indices, but five of the 18 (28%) showed overall histological improvement. Changes occurred irrespective of treatment with thioctic acid, which suggested that, over six months, this drug did not influence the course of alcohol-related liver disease.

Specific gravity adjustment of urine analysis results.

Analysis of urine samples for compounds such as lead, phenol, or 4,4'-methylene bis (2-chloroaniline) (MBOCA) are often adjusted for specific gravity following a recommendation in a NIOSH Benzene Criteria Document. The adjustment normalizes all results to a specific gravity of 1.024 by multiplying the analytical result in microgram/liter by 24/G where G is the last 2 digits of the specific gravity of the urine sample. The adjustment calculation is based on a suggestion by Levine and Fahy, who found that the urine solids content is roughly proportional to 24/G. We believe this adjustment to be inappropriate based on the following considerations.

Immunocytochemical identification of caeruloplasmin in hepatocytes of patients with Wilson's disease.

Decreased serum caeruloplasmin levels in patients with Wilson's disease have been attributed to decreased caeruloplasmin synthesis in the hepatocyte. An immunoperoxidase procedure was used to identify caeruloplasmin in liver biopsies. The pattern of staining in biopsies from patients with Wilson's disease did not differ from the pattern seen in normal adult or neonatal liver. This indicates that immunoreactive caeruloplasmin is synthesized by the liver cell in Wilson's disease. Low serum levels of caeruloplasmin may reflect an abnormality of copper incorporation into the apoprotein or an abnormality of holocaeruloplasmin export.

Aggressive chondroblastoma. Report of a case with multiple bone and soft tissue involvement.

A 14-year-old male had a recurrent chondroblastoma in his right talus which involved the right calcaneus and the soft tissue of that ankle. While the initial lesion had a typical, benign appearance, the recurrent lesion and the soft tissue nodules showed a significantly elevated mitotic rate. Although some extraosseous involvement by chondroblastomas may be secondary to soft tissue or hematogeneous seeding at the time of surgery, and aggressive variant of chondroblastoma appears to exist. Previous reports of these aggressive cases show a poor correlation between histologic appearance and biologic behavior. When objective quantitation of cytologic features such as mitotic rate are made, we believe that these features may serve as a marker for identification of those cases of chondroblastoma which have a propensity for aggressive behavior.