Effect of varying chain length between P1 and P1′ position of tripeptidomimics on activity of angiotensin-converting enzyme inhibitors

One of the efficient modes of treatments of chronic hypertension and cardiovascular disorders has been to restrain the formation of angiotensin-II by inhibiting the action of angiotensin-converting enzyme (ACE) on angiotensin-I. The efforts continue towards achieving superior molecules or drugs with improved affinities, better bioavailability and thus to achieve long duration of action with minimum side effects. Previously, we reported a library of tripeptidomimics of Ornithyl–Proline (Orn–Pro) conjugated with various unnatural amino acids and carboxylic acid derived heterocyclics based on the SAR studies of existing ACE inhibitors. Their synthesis and screening for possible inhibitors of angiotensin-converting enzyme (ACE) revealed that increase in the backbone chain length by one carbon atom results in a sudden decrease in their activity. Therefore, in the present study heterocycles with different chain length were introduced to interact with the hydrophobic S₂ sub-site of ACE and screened for their in vitro ACE inhibition activity. Further, their binding interaction with C-domain of somatic ACE was also determined. Docking and consequent LUDI scores showed good correlation with binding of these molecules in the active site of ACE. Results suggest that heterocycles with C₃ chain length are more appropriate for the effective binding of the tripeptidomimics within the active site of ACE.     

Effect of peptidyltransferase inhibitors on ribonuclease P activity from Dictyostelium discoideum – Effect of antibiotics on RNase P

The effect of several peptidyltransferase inhibitors on ribonuclease P activity from Dictyostelium discoideum was investigated. Among the inhibitors tested puromycin, amicetin and blasticidin S revealed a dose-dependent inhibition of tRNA maturation. Blasticidin S and amicetin do not compete with puromycin for the same site on the enzyme, suggesting the existence of distinct antibiotic binding sites on D. discoideum RNase P. Inhibition experiments further indicate that binding sites for blasticidin S and amicetin overlap.     

Dissociation of P13–P14 far-field potentials: clinical and MRI correlation

P13 and P14 far-field potentials are recorded over the scalp with median nerve stimulation when non-cephalic reference is used to measure somatosensory evoked potentials. The dissociation of these 2 potentials is exceptional. Only 2 cases subsequent to pontine lesions have been described hitherto. We report the case of a 31-year-old woman with a low grade gliomallocated at the spino-medullary junction who presented a P13–P14 far-field dissociation. This case fully supports the independent nature of the P13 and P14 potential generators.     

Comparative Analysis of Growth and Photosynthetic Characteristics of (Populus simonii × P. nigra) × (P. nigra × P. simonii) Hybrid Clones of Different Ploidides

To evaluate differences among poplar clones of various ploidies, 12 hybrid poplar clones (P. simonii × P. nigra) × (P. nigra × P. simonii) with different ploidies were used to study phenotypic variation in growth traits and photosynthetic characteristics. Analysis of variance showed remarkable differences for each of the investigated traits among these clones (P < 0.01). Coefficients of phenotypic variation (PCV) ranged from 2.38% to 56.71%, and repeatability ranged from 0.656 to 0.987. The Pn (photosynthetic rate) photosynthetic photon flux density (PPFD) curves of the 12 clones were S-shaped, but the Pn-ambient CO₂ (Ca) curves were shaped like an inverted “V”. The stomatal conductance (Gs)-PPFD and transpiration rate (Tr)-PPFD curves had an upward tendency; however, with increasing PFFD, the intercellular CO₂ concentration (Ci)-PPFD curves had a downward tendency in all of the clones. The Pn-PPFD and Pn-Ca curves followed the pattern of a quadratic equation. The average light saturation point and light compensation point of the triploid clones were the highest and lowest, respectively, among the three types of clones. For Pn-Ca curves, diploid clones had a higher average CO₂ saturation point and average CO₂ compensation point compared with triploid and tetraploid clones. Correlation analyses indicated that all investigated traits were strongly correlated with each other. In future studies, molecular methods should be used to analyze poplar clones of different ploidies to improve our understanding of the growth and development mechanisms of polyploidy.     

Formation of P1, P2-dinucleoside 5′-pyrophosphates under potentially prebiological conditions

Summary Organic pyrophosphates such as UppA and NAD are formed when a solution containing a nucleotide, a nucleoside 5-polyphosphate, Mg²⁺ and imidazole are allowed to dry out. We suggest that this synthesis may have occured concurrently with oligonucleotide formation.Abbreviations Im Imidazole - CDI 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride - EDTA ethylenediaminetetraacetic acid - A adenosine - U uridine - p_nA adenosine 5-poly-phosphate containing n phosphate residues - pU uridine 5-phosphate - AppA P₁,P₂-diadenosine 5-pyrophosphate - UppA P₁-(uridine 5)-P₂-(adenosine 5)-pyrophosphate - ImpA adenosine 5-phosphorimidazolide - NMN nicotinamide mononucleotide - NAD nicotinamide-adenine dinucleotide     

Chemical Synthesis of Cap Analogues: P1,P2-Dinucleoside-5′-diphosphates

Abstract

A procedure was developed for the chemical synthesis of P¹,P²-dinucleoside-5′-diphosphates (N₁(5′)pp(5′)N₂) on a nanomolar scale Reaction conditions for activating purine-5′-monophosphates (pA, pG, and pm⁷G) by 1,1′-carbonyldiimidazole were studied and optimized in respect to solvents and amount of activating reagent used. Various dinucleoside-5′-diphosphates were synthesized in 62-98% yield by incubating activated and non-activated purine-5′-monophosphates. Two unexpected by-products were formed by competition reactions: the imidazolidate of the non-activated nucleotide and the corresponding symmetrically substituted dinucleoside-5′-diphosphate. A mechanism is proposed to explain the observed side reactions.     

Bone phenotype of P2X4 receptor knockout mice: implication of a P2X7 receptor mutation?

Transgenic and knockout animal models are widely used to investigate the role of receptors, signaling pathways, and other peptides and proteins. Varying results are often published on the same model from different groups, and much effort has been put into understanding the underlying causes of these sometimes conflicting results. Recently, it has been shown that a P2X4R knockout model carries a so-called passenger mutation in the P2X7R gene, potentially affecting the interpretation of results from studies using this animal model. We therefore report this case to raise awareness about the potential pitfalls using genetically modified animal models, especially within P2 receptor research. Although purinergic signaling has been recognized as an important contributor to the regulation of bone remodeling, the process that maintains the bone quality during life, little is known about the role of the P2X4 receptor (P2X4R) in regulation of bone remodeling in health and disease. To address this, we analyzed the bone phenotype of P2rx4tm1Rass (C57BL/6J) knockout mice and corresponding wildtype using microCT and biomechanical testing. Overall, we found that the P2X4R knockout mice displayed improved bone microstructure and stronger bones in an age- and gender-dependent manner. While cortical BMD, trabecular BMD, and bone volume were higher in the 6-month-old females and 3-month-old males, this was not the case for the 3-month-old females and the 6-month-old males. Bone strength was only affected in the females. Moreover, we found that P2X4R KO mice carried the P2X7 receptor 451P wildtype allele, whereas the wildtype mice carried the 451L mutant allele. In conclusion, this study suggests that P2X4R could play a role in bone remodeling, but more importantly, it underlines the potential pitfalls when using knockout models and highlights the importance of interpreting results with great caution. Further studies are needed to verify any specific effects of P2X4R on bone metabolism.

     

Changes and availability of P fractions following 65 years of P application to a calcareous soil in a Mediterranean climate

The fate and availability of P derived from granular fertilisers in an alkaline Calcarosol soil were examined in a 65-year field trial in a semi-arid environment (annual rainfall 325 mm). Sequential P fractionation was conducted in the soils collected from the trial plots receiving 0–12 kg P ha⁻¹crop⁻¹, and the rhizosphere soil after growing wheat (Triticum aestivum L. cv. Yitpi) and chickpea (Cicer arietinum L. cv. Genesis 836) for one or two 60-day cycles in the glasshouse. Increasing long-term P application rate over 65 years significantly increased all inorganic P (Pi) fractions except HCl–Pi. By contrast, P application did not affect or tended to decrease organic P (Po) fractions. Increasing P application also increased Olsen-P and resin-P but decreased the P buffer capacity and sorption maxima. Residual P, Pi and Po fractions accounted for an average of 32, 16 and 52% of total P, respectively. All soil P fractions including residual P in the rhizosphere soil declined following 60-day growth of either wheat or chickpea. The decreases were greater in soils with a history of high P application than low P. An exception was water-extractable Po, which increased following plant growth. Changes in various P fractions in the rhizosphere followed the same pattern for both plant species. Biomass production and P uptake of the plants grown in the glasshouse correlated positively with the residual P and inorganic fractions (except HCl–Pi) but negatively with Po in the H₂O-, NaOH- and H₂SO₄-fractions of the original soils. The results suggest that the long-term application of fertiliser P to the calcareous sandy soil built up residual P and non-labile Pi fractions, but these P fractions are potentially available to crops.     

Daily Rhythms of P‐glycoprotein Expression in Mice

Recent studies have shown the gene expression of several transporters to be circadian rhythmic. However, it remains to be elucidated whether the expression of P‐glycoprotein, which is involved in the transport of many medications, undergoes 24 h rhythmicity. To address this issue, we investigated daily profiles of P‐glycoprotein mRNA and protein levels in peripheral mouse tissues. In the liver and intestine, but not in the kidney, Abcb1a mRNA expression showed clear 24 h rhythmicity. On the other hand, Abcb1b and Abcb4, the other P‐glycoprotein genes, did not exhibit significant rhythmic expression in the studied tissues. In the intestine, levels of whole P‐glycoprotein also exhibited a daily rhythm, with a peak occurring in the latter half of the light phase and a trough at the onset of the light phase. Consistent with the day‐night change of P‐glycoprotein level, the ex vivo accumulation of digoxin, an Abcb1a P‐glycoprotein substrate, into the intestinal segments at the onset of dark phase was significantly lower than it was at the onset of the light phase. Thus, Abcb1a P‐glycoprotein expression, and apparently its function, are 24 h rhythmic at least in mouse intestine tissue. This circadian variation might be involved in various chronopharmacological phenomena.     

Structural control of cytochrome P450-catalyzed ω-hydroxylation

The regiospecific or preferential ω-hydroxylation of hydrocarbon chains is thermodynamically disfavored because the ease of C–H bond hydroxylation depends on the bond strength, and the primary C–H bond of a terminal methyl group is stronger than the secondary or tertiary C–H bond adjacent to it. The hydroxylation reaction will therefore occur primarily at the adjacent secondary or tertiary C–H bond unless the protein structure specifically enforces primary C–H bond oxidation. Here we review the classes of enzymes that catalyze ω-hydroxylation and our current understanding of the structural features that promote the ω-hydroxylation of unbranched and methyl-branched hydrocarbon chains. The evidence indicates that steric constraints are used to favor reaction at the ω-site rather than at the more reactive (ω−1)-site.     

Structural characterization of P1′-diversified urea-based inhibitors of glutamate carboxypeptidase II

Urea-based inhibitors of human glutamate carboxypeptidase II (GCPII) have advanced into clinical trials for imaging metastatic prostate cancer. In parallel efforts, agents with increased lipophilicity have been designed and evaluated for targeting GCPII residing within the neuraxis. Here we report the structural and computational characterization of six complexes between GCPII and P1′-diversified urea-based inhibitors that have the C-terminal glutamate replaced by more hydrophobic moieties. The X-ray structures are complemented by quantum mechanics calculations that provide a quantitative insight into the GCPII/inhibitor interactions. These data can be used for the rational design of novel glutamate-free GCPII inhibitors with tailored physicochemical properties.     

Synthesis and Properties of P1, P2-, P1, P3- and P1, P4-Dinucleoside Di-, Tri- and Tetraphosphate mRNA 5′-Cap Analogues

Abstract

Chemically synthesized dinucleoside P¹, P²-di-, P¹, P³-tri- and P¹, P⁴-tetraphosphates, derivatives of 5′-linked 7-methylguanosine and guanosine were characterized with respect to their structural properties and functional effect on eukaryotic translation inhibition.     

Is the evolutionary history of the O-type P element in the saltans and willistoni groups of Drosophila similar to that of the canonical P element?

We studied the occurrence of O-type P elements in at least one species of each subgroup of the saltans group, in order to better understand the phylogenetic relationships among the elements within the saltans group and with those of species belonging to the willistoni group. We found that the O-type subfamily has a patchy distribution within the saltans group (it does not occur in D. neocordata and D. emarginata), low sequence divergence among species of the saltans group as well as in relation to species of the willistoni group, a lower rate of synonymous substitution for coding sequences compared to Adh, and phylogenetic incongruities. These findings suggest that the evolutionary history of the O-type subfamily within the saltans and willistoni groups follows the same model proposed for the canonical subfamily of P elements, i.e., events of horizontal transfer between species of the saltans and willistoni groups.     

Inheritance Profile of Weathered Chlordane and P,P′-DDTs Accumulation by cucurbita pepo hybrids

Cucurbita pepo ssp pepo (zucchini) accumulates significant levels of persistent organic pollutants in its roots, followed by unexpectedly high contaminant translocation to the stems. Most other plant species, including the closely related C. pepo ssp ovifera (squash), do not have this ability. To investigate the mechanism of contaminant accumulation, two cultivars each of parental zucchini and squash, as well as previously created first filial (F1) hybrids and F1 backcrosses (BC) of those parental cultivars, were grown under field conditions in a soil contaminated with weathered chlordane (2.29 μg/g) and DDX residues (0.30 μg/g; sum of DDT, DDE, DDD). The parental zucchini had stem-to-soil bioconcentration factors (BCF, contaminant ratio of stem to soil) for chlordane and DDX of 6.23 and 3.10; these values were 2.2 and 3.7 times greater than the squash, respectively. Chlordane and DDX translocation factors, the ratio of contaminant content in the stems to that in the root, were 2.1 and 3.2 times greater for zucchini than for squash. The parental zucchini and squash also differed significantly in chlordane component ratios (relative amounts of trans-nonachlor [TN], cis-chlordane [CC], trans-chlordane [TC]) and enantiomer fractions for the chiral CC and TC. Hybridization of the parental squash and zucchini resulted in significant differences in contaminant uptake. For both the three separate component ratios (CR) and two sets of enantiomer fraction (EF) values, subspecies specific differences in the parental generation became statistically equivalent in the F1 hybrid zucchini and squash. When backcrossed (BC) with the original parental plants, the zucchini and squash F1 BC cultivars reverted to the statistically distinct CR and EF patterns. This pattern of trait segregation upon hybridization suggests either single gene or single locus control for persistent organic pollutant (POP) uptake ability by C. pepo ssp pepo.     

Exploration of cathepsin S inhibitors characterized by a triazole P1–P2 amide replacement

This paper details exploration of a class of triazole-based cathepsin S inhibitors originally reported by Ellman and co-workers. SAR studies involving modifications across the whole inhibitor provide a perspective on the strengths and weaknesses of this class of inhibitors. In addition, we put the unique characteristics of this class of compounds into perspective with other classes of cathepsin S inhibitors.     

The phosphorus concentration of common rocks—a potential driver of ecosystem P status

Background

Soil phosphorus (P) availability can be an important regulator of ecosystem processes. Changes in P availability over time have long been studied, but the P concentration of soil parent materials—which determines ecosystem P concentration at the onset of soil formation—have never been systematically explored. Here we ask two questions: 1) how does P concentration vary among soil parent materials? and 2) under what range of conditions do those differences influence soil P concentration?

Methods

We used the Earthchem webportal to compile the P concentration of 263,539 rocks. We then gathered data from 62 sites (MAT ranging from 200–5,000 mm?yr^-1 and soil age from 0.3–4,100 ky) and assessed the correlation between rock and soil P concentration.

Results

We found a 30 fold difference in median P concentration among rock types, ranging from 120 ppm (several ultramafic rocks) to >3,000 ppm (several alkali basalts). Median P was significantly lower in common silica-rich rocks (e.g. granite - 436 ppm) and higher in common iron-rich rocks (e.g. andesite - 1,000 ppm). In sedimentary rocks, which make up 70 % of the ice-free land surface, median P was highest in mudstone (1,135 ppm) and decreased with increasing grainsize (siltstone-698 ppm, sandstone-500 ppm). Where soil P and parent material P were measured in the same site, parent material P explained 42 % of the variance in total soil P (n?=?62), and explanatory power was higher for sites with similar climate.

Conclusion

The variation in P concentration among common rock types is on a comparable scale to the changes in total P, and several P pools, over long-term soil development. Quantifying these differences may be an important step towards characterizing regional and global variation in soil and ecosystem P status.     

Factors controlling long-term changes of the eutrophicated ecosystem of Pärnu Bay,Gulf of Riga

Phytoplankton, mesozooplankton, mysids and fish larvae were studied during 15–29 annual cycles measured weekly to monthly in Pärnu Bay, the Gulf of Riga. The monthly variability of the biological data was related to temperature, ice conditions, salinity, influx of nutrients, the North Atlantic Oscillation (NAO) index, cloudiness and solar activity. Phytoplankton development was mainly a function of the NAO index. For the whole study period the abundance of zooplankton increased with increasing water temperature and solar activity. Significant correlations between phytoplankton and zooplankton densities were found until 1990. After the invasion of the predatory cladoceran Cercopagis pengoi in 1991, the zooplankton community was likely to be regulated by the introduced species rather than phytoplankton dynamics. The increased abundances of rotifers and copepods triggered the increase in mysid densities. The development of herring larvae was positively affected by the high density of copepods and rotifers but also by increased eutrophication. Until 1990 there was no significant relationship between the density of zooplankton and herring larvae. A negative relationship between the density of zooplankton and herring larvae in the 1990s suggests that the major shift in zooplankton community resulted in food limitation for herring larvae. The results indicated that (1) atmospheric processes in the northern Atlantic explain a large part of the interannual variation of the local phytoplankton stock, (2) trophic interactions control the development of pelagic communities at higher trophic levels, and (3) the introduction of an effective intermediate predator has repercussions for the whole pelagic food web in Pärnu Bay.     

Characterization of bacteriophage P1 library containing inserts of Drosophila DNA of 75–100 kilobase pairs

A multiple-hit bacteriophage P1 library containing DNA fragments from Drosophila melanogaster in the size range 75–100 kb was created and subjected to a preliminary evaluation for completeness, randomness, fidelity, and clone stability. This P1 library presently contains 3840 individual clones, or approximately two genome equivalents. The library was screened with a small set of unique-sequence test probes, and clones containing the sequences have been recovered. In situ hybridization with salivary gland chromosomes indicates that the clones originate from the site of the probe sequences in the genome, and filter hybridization of restriction digests suggests that the clones are not rearranged in comparison with the genomic sequences. Approximately 1.7% of the clones contain sequences that hybridize with ribosomal DNA. A small subset of these clones was tested for stability by examination of restriction fragments produced after repeated subculturing, and no evidence for instability was found. The P1 cloning system has general utility in molecular genetics and may provide an important intermediate level of resolution in physical mapping of the Drosophila genome.by W. Hennig