A non-covalent peptide-based carrier for in vivo delivery of DNA mimics

The dramatic acceleration in identification of new nucleic-acid-based therapeutic molecules has provided new perspectives in pharmaceutical research. However, their development is limited by their poor cellular uptake and inefficient trafficking. Here we describe a short amphipathic peptide, Pep-3, that combines a tryptophan/phenylalanine domain with a lysine/arginine-rich hydrophilic motif. Pep-3 forms stable nano-size complexes with peptide-nucleic acid analogues and promotes their efficient delivery into a wide variety of cell lines, including primary and suspension lines, without any associated cytotoxicity. We demonstrate that Pep-3-mediated delivery of antisense-cyclin B1-charged-PNA blocks tumour growth in vivo upon intratumoral and intravenous injection. Moreover, we show that PEGylation of Pep-3 significantly improves complex stability in vivo and consequently the efficiency of antisense cyclin B1 administered intravenously. Given the biological characteristics of these vectors, we believe that peptide-based delivery technologies hold a true promise for therapeutic applications of DNA mimics.     

Cardioprotection from ischemia-reperfusion injury due to Ras-GTPase inhibition is attenuated by glibenclamide in the globally ischemic heart

The present study was designed to see if acute local inhibition of Ras-GTPase before or after ischemia (during perfusion) would produce protection against ischemia and reperfusion (I/R)-induced cardiac dysfunction. The effect of glibenclamide, an inhibitor of cardiac mitochondrial ATP-sensitive potassium (mitoK(ATP)) channels, on Ras-GTPase-mediated cardioprotection was also studied. A 40 min episode of global ischemia followed by a 30 min reperfusion in perfused rat hearts produced significantly impaired cardiac function, measured as left ventricular developed pressure (P(max)) and left ventricular end-diastolic pressure (LVEDP). Perfusion with Ras-GTPase inhibitor FPT III before I/R [FPT(pre)], significantly enhanced cardiac recovery in terms of left ventricular contractility. P(max) was significantly higher at the end of 30 min reperfusion in FPT(pre)-treated hearts compared to pre-conditioned hearts. However, the degree of improvement in left ventricular contractility was significantly less when FPT III was given only after ischemia during reperfusion [FPT(post)]. Combination treatment with FPT III and glibenclamide before I/R resulted in significant reduction of FPT III-mediated cardioprotection. These data suggest that activation of Ras-GTPase signaling pathways during ischemia are critical in the development of left ventricular dysfunction and that opening of mitoK(ATP) channels, at least in part, contributes to cardioprotection produced by Ras-GTPase inhibition.     

Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility

A reduced protein model combined with a systematic docking approach has been employed to predict protein-protein complex structures in CAPRI rounds 6-11. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to the second protein starting from many thousand initial protein partner placements. It also allows for approximate inclusion of global flexibility of protein partners during systematic docking by conformational relaxation of the partner proteins in precalculated soft collective backbone degrees of freedom. We have submitted models for six targets, achieved acceptable docking solutions for two targets, and predicted >20% correct contacts for five targets. Possible improvements of the docking approach in particular at the scoring and refinement steps are discussed.     

CCR5 receptor antagonists: discovery and SAR of novel 4-hydroxypiperidine derivatives

The guanylhydrazone of 2-(4-chlorobenzyloxy)-5-bromobenzaldehyde, 1, with an IC(50) of 840 nM against the CCR5 receptor was identified using high-throughput screening. Optimization efforts led to the discovery of a novel piperidine series of CCR5 antagonists. In particular, the 4-hydroxypiperidine derivative, 6k, had improved potency against CCR5, and was a starting point for further optimization. SAR elaboration using parallel synthesis led to the identification of 10h, a potent CCR5 antagonist with an IC(50) of 11 nM.     

(Glyco)sphingolipidology: an amazing challenge and opportunity for systems biology

Sphingolipids are found in essentially all eukaryotes and in some prokaryotes and viruses, where they influence cell structure, signaling and interactions with the extracellular environment. Because of the combinatorial nature of their biosynthesis, the sphingolipidome comprises untold thousands of species that encompass bioactive backbones and complex phospho- and glycolipids. Mass spectrometry is able to analyze a growing fraction of the sphingolipidome and is beginning to provide information about localization. Use of these structure specific, quantitative methods is producing insights, and surprises, regarding sphingolipid structure, metabolism, function and disease. Dealing with such large data sets poses special challenges for systems biology, but the intrinsic and elegant interrelationships among these compounds might provide a key to dealing with the complexity of the sphingolipidome.     

Nonparametric tests for two-group comparisons of dependent observations obtained at varying time points

We propose new tests for two-group comparisons of repeated measures of a response where the repeated measures might be obtained at arbitrary time points that differ over individuals. The tests are almost U-statistics in that the kernel contains some unknown parameters that need to be estimated from the data. Our methods are designed for settings in which response means of one group are strictly greater than the response means of the other group. The tests do not make any assumptions regarding the distribution of the repeated measures except that one of the tests assumes that the repeated measures can be grouped into distinct periods of observations (e.g., around fixed follow-up time points) such that the covariance between scores only depends on the periods the observations belong to and that the covariance matrices are the same in the two groups. The tests are valid even if the probability that a response is observed depends on the level of response provided that the missing data mechanism is the same in both groups. Inference can conveniently be based on resampling. We provide asymptotic results for the test statistics. We investigate size and power of the tests and use them to assess differences in viral load decline for drug-resistant and drug-sensitive human immunodeficiency virus (HIV)-1 infected patients.     

Tryptathionine bridges in peptide synthesis

The tryptathionine linkage is a crosslink formed between tryptophan and cysteine. This feature is characteristic of the bicyclic peptides: the phallotoxins and the amatoxins. These peptides both bind to protein folds of their respective targets (F-actin and RNA pol II, respectively) with extremely high affinities. Studies on these peptides have shown that the tryptathionine crosslink is essential for this binding affinity. Tryptathionines have been investigated for many years and several syntheses exist for their formation. In this review, we report on the various methodologies employed in tryptathionine synthesis, and discuss some of the advantages and disadvantages associated with each of them.     

Assessment of dynamic changes in cerebral autoregulation.

Cerebral autoregulation (CA) is a control mechanism that adjusts cerebral vasomotor tone in response to changes in arterial blood pressure (ABP) to ensure a nearly constant cerebral blood flow. Patient treatment could be optimized if CA monitoring were possible. Whereas the concept of static CA assessment is simply based on comparison of mean values obtained from two stationary states (e.g., before and after a pressure change), the evaluation of dynamic CA is more complex. Among other methods, moving cross-correlation analysis of slow waves in ABP and cerebral blood flow velocity (CBFV) seems to be appropriate to monitor CA quasi-continuously. The calculation of an "instantaneous transfer function" between ABP and CBFV oscillations in the low-frequency band using the Wigner-Ville distribution may represent an acceptable compromise in time-frequency resolution for continuous CA monitoring.     

Functional analysis of a beta-1,6-glucanase gene from the grass endophytic fungus Epichloë festucae

β-1,6-glucanases degrade the polysaccharide β-1,6-glucan, a cell wall component in some filamentous fungi. A single copy of a β-1,6-glucanase gene, designated gcnA, was identified in each of the grass endophytic fungi Neotyphodium lolii and Epichloë festucae. Phylogenetic analysis indicates that the GcnA protein is a member of glycosyl hydrolase family 5, and is closely related to fungal β-1,6-glucanases implicated in mycoparasitism. The E. festucae gcnA gene was expressed in mycelium grown in culture and in both vegetative and reproductive tissues of perennial ryegrass. A gcnA replacement mutant had reduced β-1,6-glucanase activity when grown in media containing pustulan as the major carbon source. β-1,6-glucanase activity was restored in the replacement mutant by introducing multiple copies of the gcnA gene. Growth of ΔgcnA and gcnA-overexpressing strains in vegetative grass tissues was indistinguishable from wild type strains.