Investigating the pharmacodynamic durability of GalNAc–siRNA conjugates

One hallmark of trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNAs is the remarkable durability of silencing that can persist for months in preclinical species and humans. Here, we investigated the underlying biology supporting this extended duration of pharmacological activity. We found that siRNA accumulation and stability in acidic intracellular compartments is critical for long-term activity. We show that functional siRNA can be liberated from these compartments and loaded into newly generated Argonaute 2 protein complexes weeks after dosing, enabling continuous RNAi activity over time. Identical siRNAs delivered in lipid nanoparticles or as GalNAc conjugates were dose-adjusted to achieve similar knockdown, but only GalNAc–siRNAs supported an extended duration of activity, illustrating the importance of receptor-mediated siRNA trafficking in the process. Taken together, we provide several lines of evidence that acidic intracellular compartments serve as a long-term depot for GalNAc–siRNA conjugates and are the major contributor to the extended duration of activity observed in vivo.     

Solution structure and folding characteristics of the C-terminal SH3 domain of c-Crk-II

Crk-II is a signaling adaptor protein that is involved in many cellular processes including apoptosis, proliferation, and differentiation. It has a modular domain architecture consisting of an Src homology 2 domain (SH2) followed by two Src homology 3 (SH3) domains. The structures and ligand-binding properties of the SH2 and the middle SH3 domains are well-characterized. Several studies suggest that the C-terminal SH3 domain plays an important regulatory role in the protein; however, no structural information is available on this domain, and relatively little is known about its binding partners. In the current work, we have solved the solution NMR structure of the C-terminal SH3 domain. The domain adopts the standard SH3 fold comprising a five-stranded beta barrel. In agreement with alignment and modeling studies, the structure indicates that the canonical-binding surface of the SH3 domain is unusually polar and suggests that this domain may not bind typical PXXP ligands or that it may bind them with reduced affinity. Thermodynamic and kinetic studies show that the domain folds in a reversible two-state manner and that the stability of the fold is similar to that observed for other SH3 domains. These studies offer some insight into the likely structural and thermodynamic consequences of point mutations in the cSH3 domain that are known to deregulate Crk-II function. Our results set the stage for a better understanding the role of the cSH3 domain in the context of the full-length protein.     

Thiostrepton induced proteins in Streptomyces, Amycolatopsis and Nocardia species

Abstract Thiostrepton-induced proteins have been observed in several actinomycetes, including Streptomyces clavuligerus (15 kDa protein), S. griseus (21 kDa), Nocardia lactamdurans (17 kDa), Amycolatopsis sp 239 (14 and 16 kDa), S. fradie (18 and 20 kDa) and S. coelicolor (17, 19, 30 and 56 kDa). The thiostrepton-induced proteins of S. coelicolor seem to be identical to those reported in S. lividans . The induction of the 18 and 20 kDa proteins of S. fradiae (up to 20% of the total protein in the cells) was dependent upon the concentration of thiostrepton (1 to 50 μg per ml) added to the cultures. The induction of proteins by thiostrepton in N. lactamdurans (and probably in the other actinomycetes as well) is not mediated by the tsr gene of pIJ702, since spontaneous thiostrepton-resistant mutants of N. lactamdurans which do not carry the tsr gene were used for the induction studies. Induction of proteins by thiostrepton may be a protective mechanism to counteract the strong effect of this antibiotic which is known to be produced by several soil microorganisms.     

Tailoring SOFC Electrode Microstructures for Improved Performance

The key technical challenges that fuel cell developers need to address are performance, durability, and cost. All three need to be achieved in parallel; however, there are often competitive tensions, e.g., performance is achieved at the expense of durability. Stability and resistance to degradation under prolonged operation are key parameters. There is considerable interest in developing new cathodes that are better able to function at lower temperature to facilitate low cost manufacture. For anodes, the ability of the solid oxide fuel cell (SOFC) to better utilize commonly available fuels at high efficiency, avoid coking and sulfur poisoning or resistance to oxidation at high utilization are all key. Optimizing a new electrode material requires considerable process development. The use of solution techniques to impregnate an already optimized electrode skeleton, offers a fast and efficient way to evaluate new electrode materials. It can also offer low cost routes to manufacture novel structures and to fine tune already known structures. Here impregnation methodologies are discussed, spectral and surface characterization are considered, and the recent efforts to optimize both cathode and anode functionalities are reviewed. Finally recent exemplifications are reviewed and future challenges and opportunities for the impregnation approach in SOFCs are explored.     

Expression of the sigmaF-directed csfB locus prevents premature appearance of sigmaG activity during sporulation of Bacillus subtilis

During sporulation, σ^G becomes active in the prespore upon the completion of engulfment. We show that the inactivation of the σ^F-directed csfB locus resulted in premature activation of σ^G. CsfB exerted control distinct from but overlapping with that exerted by LonA to prevent inappropriate σ^G activation. The artificial induction of csfB severely compromised spore formation.     

Toluene toxicity: Effects of sublethal levels on enzyme activities in seawater adapted tilapia(Sarotherodon mossambicus Peters)

The effects of exposing seawater adapted cichlid fish, tilapia(Sarotherodon mossambicus Peters) to sublethal concentrations of toluene on the activities of lactate dehydrogenase, succinate dehydrogenase and acetylcholinesterase were studied. The activity of lactate dehydrogenase increased while those of succinate dehydrogenase and acetylcholinesterase were inhibited in most tissues of the exposed fish. The alterations in the dehydrogenases suggested that some changes in carbohydrate metabolism may have occurred. Acetylcholinesterase inhibition in brain and other tissues indicated impairment of nervous function in toluene-intoxicated tilapia.     

Structure-based virtual screening,molecular docking,ADMET and molecular simulations to develop benzoxaborole analogs as potential inhibitor against Leishmania donovani trypanothione reductase

Visceral leishmaniasis (VL) is the most fatal form of leishmaniasis and it affects 70 countries worldwide. Increasing drug resistant for antileishmanial drugs such as miltefosine, sodium stibogluconate and pentamidine has been reported in the VL endemic region. Amphotericin B has shown potential antileishmanial activity in different formulations but its cost of treatment and associated nephrotoxicity have limited its use by affected people living in the endemic zone. To control the VL infection in the affected countries, it is necessary to develop new antileishmanial compounds with high efficacy and negligible toxicity. Computer aided programs such as binding free energy estimation; ADMET prediction and molecular dynamics simulation can be used to investigate novel antileishmanial molecules in shorter duration. To develop antileishmanial lead molecule, we performed standard precision (SP) docking for 1160 benzoxaborole analogs along with reference inhibitors against trypanothione reductase of Leishmania parasite. Furthermore, extra precision (XP) docking, ADMET prediction, prime MM-GBSA was conducted over 115 ligands, showing better docking score than reference inhibitors to get potential antileishmanial compounds. Simultaneously, area under the curve (AUC) was estimated using ROC plot to validate the SP and XP docking protocol. Later on, two benzoxaborole analogs with best MM-GBSA ΔG-bind were subjected to molecular simulation and docking confirmation to ensure the ligand interaction with TR. The presented drug discovery based on computational study confirms that BOB27 can be used as a potential drug candidate and warrants further experimental investigation to fight against VL in endemic areas.     

Zeptomole detection of a viral nucleic acid using a target-activated ribozyme

We describe a strategy for the ultra-sensitive detection of nucleic acids using "half" ribozymes that are devoid of catalytic activity unless completed by a trans-acting target nucleic acid. The half-ribozyme concept was initially demonstrated using a construct derived from a multiple turnover Class I ligase. Iterative RNA selection was carried out to evolve this half-ribozyme into one activated by a conserved sequence present in the hepatitis C virus (HCV) genome. Following sequence optimization of substrate RNAs, this HCV-activated half-ribozyme displayed a maximal turnover rate of 69 min(-1) (pH 8.3) and was induced in rate by approximately 2.6 x 10(9)-fold by the HCV target. It detected the HCV target oligonucleotide in the zeptomole range (6700 molecules), a sensitivity of detection roughly 2.6 x 10(6)-fold greater than that previously demonstrated by oligonucleotide-activated ribozymes, and one that is sufficient for molecular diagnostic applications.     

Control of the expression and compartmentalization of (sigma)G activity during sporulation of Bacillus subtilis by regulators of (sigma)F and (sigma)E

During formation of spores by Bacillus subtilis the RNA polymerase factor sigma(G) ordinarily becomes active during spore formation exclusively in the prespore upon completion of engulfment of the prespore by the mother cell. Formation and activation of sigma(G) ordinarily requires prior activity of sigma(F) in the prespore and sigma(E) in the mother cell. Here we report that in spoIIA mutants lacking both sigma(F) and the anti-sigma factor SpoIIAB and in which sigma(E) is not active, sigma(G) nevertheless becomes active. Further, its activity is largely confined to the mother cell. Thus, there is a switch in the location of sigma(G) activity from prespore to mother cell. Factors contributing to the mother cell location are inferred to be read-through of spoIIIG, the structural gene for sigma(G), from the upstream spoIIG locus and the absence of SpoIIAB, which can act in the mother cell as an anti-sigma factor to sigma(G). When the spoIIIG locus was moved away from spoIIG to the distal amyE locus, sigma(G) became active earlier in sporulation in spoIIA deletion mutants, and the sporulation septum was not formed, suggesting that premature sigma(G) activation can block septum formation. We report a previously unrecognized control in which SpoIIGA can prevent the appearance of sigma(G) activity, and pro-sigma(E) (but not sigma(E)) can counteract this effect of SpoIIGA. We find that in strains lacking sigma(F) and SpoIIAB and engineered to produce active sigma(E) in the mother cell without the need for SpoIIGA, sigma(G) also becomes active in the mother cell.