Identification of specific features of inhibition of PKCβII and its potential lead by shape-based virtual screening and molecular docking studies

Protein kinase C βII (PKCβII) is preferentially expressed during hyperglycemic state resulting in diabetic complications, particularly, diabetic cardiomyopathy. An effective inhibition of PKCβII is a potential option to directly treat the diabetic cardiomyopathy; however, till date no efficient drug targeting PKCβII is available and all the reported PKCβII ligands are maleimide derivatives. The purpose of the present work is to study the importance of the maleimide moiety in PKCβII inhibition and the effects that follow after replacing the maleimide with similar moiety on PKCβII inhibition. For this, an in-house database of maleimide analogues was prepared and shape based screening of commercial databases viz. Specs2009, NCI2003 was performed, followed by filtration using virtual filters. The binding features of reported PKCβII inhibitors, and high scoring hits were analyzed with the help of molecular docking studies. The features identified from the above studies were used for the rational design of new PKCβII inhibitors. The molecular dynamics simulation and ligand-receptor binding affinity studies of the designed molecules has been reported. The toxicity of all the shortlisted and designed molecules was predicted.     

Identification of Endophilins 1 and 3 as Selective Binding Partners for VGLUT1 and Their Co-Localization in Neocortical Glutamatergic Synapses: Implications for Vesicular Glutamate Transporter Trafficking and Excitatory Vesicle Formation

1. Selective protein–protein interactions between neurotransmitter transporters and their synaptic targets play important roles in regulating chemical neurotransmission. We screened a yeast two-hybrid library with bait containing the C-terminal amino acids of VGLUT1 and obtained clones that encode endophilin 1 and endophilin 3, proteins considered to play an integral role in glutamatergic vesicle formation.2. Using a modified yeast plasmid vector to enable more cost-effective screens, we analyzed the selectivity and specificity of this interaction. Endophilins 1 and 3 selectively recognize only VGLUT1 as the C-terminus of VGLUT2 and VGLUT3 do not interact with either endophilin isoform. We mutagenized four conserved stretches of primary sequence in VGLUT1 that includes two polyproline motifs (Pro1, PPAPPP, and Pro2, PPRPPPP), found only in VGLUT1, and two conserved stretches (SEEK, SYGAT), found also in VGLUT2 and VGLUT3. The absence of the VGLUT conserved regions does not affect VGLUT1–endophilin association. Of the two polyproline stretches, only one (Pro2) is required for binding specificity to both endophilin 1 and endophilin 3.3. We also show that endophilin 1 and endophilin 3 co-localize with VGLUT1 in synaptic terminals of differentiated rat neocortical neurons in primary culture. These results indicate that VGLUT1 and both endophilins are enriched in a class of excitatory synaptic terminals in cortical neurons and there, may interact to play an important role affecting the vesicular sequestration and synaptic release of glutamate.     

Persistence of Mycobacterium avium subsp. paratuberculosis and Other Zoonotic Pathogens during Simulated Composting, Manure Packing, and Liquid Storage of Dairy Manure

Livestock manures contain numerous microorganisms which can infect humans and/or animals, such as Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., and Mycobacterium avium subsp. paratuberculosis (Mycobacterium paratuberculosis). The effects of commonly used manure treatments on the persistence of these pathogens have rarely been compared. The objective of this study was to compare the persistence of artificially inoculated M. paratuberculosis, as well as other naturally occurring pathogens, during the treatment of dairy manure under conditions that simulate three commonly used manure management methods: thermophilic composting at 55°C, manure packing at 25°C (or low-temperature composting), and liquid lagoon storage. Straw and sawdust amendments used for composting and packing were also compared. Manure was obtained from a large Ohio free-stall dairy herd and was inoculated with M. paratuberculosis at 10⁶ CFU/g in the final mixes. For compost and pack treatments, this manure was amended with sawdust or straw to provide an optimal moisture content (60%) for composting for 56 days. To simulate liquid storage, water was added to the manure (to simulate liquid flushing and storage) and the slurry was placed in triplicate covered 4-liter Erlenmeyer flasks, incubated under ambient conditions for 175 days. The treatments were sampled on days 0, 3, 7, 14, 28, and 56 for the detection of pathogens. The persistence of M. paratuberculosis was also assessed by a PCR hybridization assay. After 56 days of composting, from 45 to 60% of the carbon in the compost treatments was converted to CO₂, while no significant change in carbon content was observed in the liquid slurry. Escherichia coli, Salmonella, and Listeria were all detected in the manure and all of the treatments on day 0. After 3 days of composting at 55°C, none of these organisms were detectable. In liquid manure and pack treatments, some of these microorganisms were detectable up to 28 days. M. paratuberculosis was detected by standard culture only on day 0 in all the treatments, but was undetectable in any treatment at 3 and 7 days. On days 14, 28, and 56, M. paratuberculosis was detected in the liquid storage treatment but remained undetectable in the compost and pack treatments. However, M. paratuberculosis DNA was detectable through day 56 in all treatments and up to day 175 in liquid storage treatments. Taken together, the results indicate that high-temperature composting is more effective than pack storage or liquid storage of manure in reducing these pathogens in dairy manure. Therefore, thermophilic composting is recommended for treatment of manures destined for pathogen-sensitive environments such as those for vegetable production, residential gardening, or application to rapidly draining fields.     

Inhibition of H-Ras and MAPK is compensated by PKC-dependent pathways in annexin A6 expressing cells

High-density lipoprotein (HDL)-induced activation of the Ras/MAPK pathway can be mediated by protein kinase C (PKC)-dependent and independent pathways. Although both pathways co-exist in cells, we showed that binding of HDL to scavenger receptor BI (SR-BI) in CHO cells activates Ras and MAPK in a PKC-independent manner. We have recently identified that HDL-induced activation of Ras and Raf-1 is reduced in annexin A6 expressing CHO cells (CHOanx6). In the present study we demonstrate that despite the loss of Ras and Raf-1 activity, HDL induces MAPK phosphorylation in CHOanx6 cells. Since annexin A6 is a PKCalpha-binding protein we therefore investigated the possible involvement of PKC in HDL-induced Ras and MAPK activation in CHOanx6 cells. Taken together our findings demonstrate that HDL-induced H-Ras and MAPK activation is PKC-dependent in cells expressing annexin A6 to compensate for the loss of PKC-independent activation of H-Ras and MAPK.     

Toxicity of the entomopathogenic bacteria Photorhabdus and Xenorhabdus to the mushroom mite (Luciaphorus sp.; Acari: Pygmephoridae)

The mushroom mite, Luciaphorus sp. is a serious pest of tropical mushrooms. We determined the pathogenicity and toxicity of species and strains of the entomopathogenic bacteria, Photorhabdus and Xenorhabdus to the mite. As these bacteria are known to produce antifungal substances, we first determined the effect of 21 species and strains of the bacteria on the mycelial growth of the mushroom, Lentinus squarrosulus. We then determined the toxicity of the eight species and strains of bacteria that did not show any effect on mushroom growth against both the female and male mites. All eight species and strains of the bacteria were toxic to the female mite resulting in significant mite mortality within 24-48 h. Cell-free supernatants from all the eight bacterial species and strains were also toxic to the female mite inflicting significant mortality within 24-48 h. The supernatants of two strains, GPS12 and GPS11, of Photorhabdus luminescens ssp. laumondii were significantly more toxic than the other species and strains to the female mite, resulting in 90-95% mite mortality within 48 h. Both the concentration and age of the bacteria had significant effect on the toxicity of the supernatants to the female mite. None of the bacteria showed toxicity to the male mite which has undeveloped mouthparts. These results indicate that P. luminescens ssp. laumondii and its byproducts are directly toxic to the female mite, suggesting the potential of developing a novel biological approach for the control of this mushroom pest. This is the first report on the miticidal activity of the entomopathogenic bacteria, Photorhabdus and Xenorhabdus.     

Annexins — Modulators of EGF receptor signalling and trafficking

At the cell surface, activation of the epidermal growth factor (EGF) receptor triggers a complex network of signalling events that regulate a variety of cellular processes. For signal termination, the activated EGF receptor is internalised and targeted to lysosomes for degradation. Microdomain localization at the plasma membrane and endocytic transport of the EGFR is important for the formation of compartment-specific signalling complexes and is regulated by scaffolding and targeting proteins. This includes Ca²⁺-effector proteins, such as calmodulin and annexins (Anx), in particular AnxA1, AnxA2, AnxA6 and as shown recently, AnxA8. Given that these annexins show differences in their expression patterns, subcellular localization and mode of action, they are likely to differentially contribute and cooperate in the fine-tuning of EGFR activity. In support of this hypothesis, current literature suggests these annexins to be involved in different steps that control the endocytic transport and signalling of the EGF receptor. This review summarizes how the coordinated activity of AnxA1, AnxA2, AnxA6 and AnxA8 can contribute to regulate EGF receptor localization and activity.     

In-Depth Molecular Characterization of Mycobacterium tuberculosis from New Delhi – Predominance of Drug Resistant Isolates of the ‘Modern’ (TbD1?) Type

Background

India has the highest estimated burden of tuberculosis in the world, accounting for 21% of all tuberculosis cases world-wide. However, due to lack of systematic analysis using multiple markers the available information on the genomic diversity of Mycobacterium tuberculosis in India is limited.

Methodology/Principal Findings

Thus, 65 M. tuberculosis isolates from New Delhi, India were analyzed by spoligotyping, MIRU-VNTR, large deletion PCR typing and single nucleotide polymorphism analysis (SNP). The Central Asian (CAS) 1 _DELHI sub-lineage was the most prevalent sub-lineage comprising 46.2% (n = 30) of all isolates, with shared-type (ST) 26 being the most dominant genotype comprising 24.6% (n = 16) of all isolates. Other sub-lineages observed were: East-African Indian (EAI)-5 (9.2%, n = 6), EAI6_BGD1 (6.2%, n = 4), EAI3_IND, CAS and T1 with 6.2% each (n = 4 each), Beijing (4.6%, n = 3), CAS2 (3.1%, n = 2), and X1 and X2 with 1 isolate each. Genotyping results from five isolates (7.7%) did not match any existing spoligopatterns, and one isolate, ST124, belonged to an undefined lineage. Twenty-six percent of the isolates belonged to the TbD1+ PGG1 genogroup. SNP analysis of the pncA gene revealed a CAS-lineage specific silent mutation, S65S, which was observed for all CAS-lineage isolates (except two ST26 isolates) and in 1 orphan. Mutations in the pncA gene, conferring resistance to pyrazinamide, were observed in 15.4% of all isolates. Collectively, mutations in the rpoB gene, the katG gene and in both rpoB and katG genes, conferring resistance to rifampicin and isoniazid, respectively, were more frequent in CAS1_DELHI isolates compared to non-CAS_DELHI isolates (OR: 3.1, CI95% [1.11, 8.70], P = 0.045). The increased frequency of drug-resistance could not be linked to the patients'' history of previous anti-tuberculosis treatment (OR: 1.156, CI95% [0.40, 3.36], P = 0.79). Fifty-six percent of all new tuberculosis patients had mutations in either the katG gene or the rpoB gene, or in both katG and rpoB genes.

Conclusion

CAS1_DELHI isolates circulating in New Delhi, India have a high frequency of mutations in the rpoB and katG genes. A silent mutation (S65S) in the pncA gene can be used as a putative genetic marker for CAS-lineage isolates.     

Insulin/TOR signaling in growth and homeostasis: a view from the fly world

The insulin/TOR pathway is a conserved regulator of cell and organism growth in metazoans. Over the last several years, an array of signaling inputs to this pathway has been defined. However the growth-regulatory outputs are less clear. Drosophila has proven to be a powerful genetic model system in which to study insulin/TOR signaling. This review highlights recent studies in Drosophila that have identified essential outputs and key effectors of the pathway. These include the regulation of ribosome synthesis, mRNA translation, autophagy and endocytosis, through downstream effectors such as Myc, FOXO, HIF1-alpha, TIF-IA, 4EBP and Atg1. This network of outputs and effectors can regulate cell and organismal metabolism, and is essential for the control of tissue growth, responses to starvation and stress, and aging. The mechanisms identified in Drosophila likely operate in most metazoans, and are relevent to our understanding of diseases caused by aberrent insulin/TOR signaling such as cancer, diabetes and obesity.