Combinatorial Virtual Library Screening Study of Transforming Growth Factor-β2–Chondroitin Sulfate System

Transforming growth factor-beta (TGF-β), a member of the TGF-β cytokine superfamily, is known to bind to sulfated glycosaminoglycans (GAGs), but the nature of this interaction remains unclear. In a recent study, we found that preterm human milk TGF-β2 is sequestered by chondroitin sulfate (CS) in its proteoglycan form. To understand the molecular basis of the TGF-β2–CS interaction, we utilized the computational combinatorial virtual library screening (CVLS) approach in tandem with molecular dynamics (MD) simulations. All possible CS oligosaccharides were generated in a combinatorial manner to give 24 di- (CS02), 192 tetra- (CS04), and 1536 hexa- (CS06) saccharides. This library of 1752 CS oligosaccharides was first screened against TGF-β2 using the dual filter CVLS algorithm in which the GOLDScore and root-mean-square-difference (RMSD) between the best bound poses were used as surrogate markers for in silico affinity and in silico specificity. CVLS predicted that both the chain length and level of sulfation are critical for the high affinity and high specificity recognition of TGF-β2. Interestingly, CVLS led to identification of two distinct sites of GAG binding on TGF-β2. CVLS also deduced the preferred composition of the high specificity hexasaccharides, which were further assessed in all-atom explicit solvent MD simulations. The MD results confirmed that both sites of binding form stable GAG–protein complexes. More specifically, the highly selective CS chains were found to engage the TGF-β2 monomer with high affinity. Overall, this work present key principles of recognition with regard to the TGF-β2–CS system. In the process, it led to the generation of the in silico library of all possible CS oligosaccharides, which can be used for advanced studies on other protein–CS systems. Finally, the study led to the identification of unique CS sequences that are predicted to selectively recognize TGF-β2 and may out-compete common natural CS biopolymers.     

Plant-derived polyphenols attenuate lipopolysaccharide-induced nitric oxide and tumour necrosis factor production in murine microglia and macrophages

Lipopolysaccharides released during bacterial infections induce the expression of pro-inflammatory cytokines and lead to complications such as neuronal damage in the CNS and septic shock in the periphery. While the initial infection is treated by antibiotics, anti-inflammatory agents would be advantageous add-on medications. In order to identify such compounds, we have compared 29 commercially available polyphenol-containing plant extracts and pure compounds for their ability to prevent LPS-induced up-regulation of NO production. Among the botanical extracts, bearberry and grape seed were the most active preparations, exhibiting IC(50) values of around 20 mug/mL. Among the pure compounds, IC(50) values for apigenin, diosmetin and silybin were 15, 19 and 12 muM, in N-11 murine microglia, and 7, 16 and 25 muM, in RAW 264.7 murine macrophages, respectively. In addition, these flavonoids were also able to down-regulate LPS-induced tumour necrosis factor production. Structure-activity relationships of the flavonoids demonstrated three distinct principles: (i) flavonoid-aglycons are more potent than the corresponding glycosides, (ii) flavonoids with a 4'-OH substitution in the B-ring are more potent than those with a 3'-OH-4'-methoxy substitution, (iii) flavonoids of the flavone type (with a C2=C3 double bond) are more potent than those of the flavanone type (with a at C2-C3 single bond).     

Numerical investigation on thrust production and unsteady mechanisms of three-dimensional oscillating wing

Journal of Mechanical Science and Technology - The thrust production of an oscillating wing in the low Reynolds number regime (75 ≤ Re ≤ 1000) was investigated via threedimensional...     

Irradiation Target Cooling Using Circular/Slot Air Jet

To study the effect of irradiation on materials, sample coupons are irradiated in cyclotron facilities. During the irradiation process, these samples produce significant heat. This heat needs to be continuously removed from the samples in order to avoid melting of the samples as well as to keep the samples at a particular temperature during irradiation. The area available for heat transfer is limited due to small size of the samples. To increase the heat transfer rate, jet cooling is used as it provides large heat transfer co-efficient. To understand the heat transfer characteristics of jet cooling under these conditions, experiments have been carried out. Two inclined jets hitting on both sides of the target plate give maximum cooling and uniform temperature distribution. This paper gives the details of the numerical and experimental studies carried out and the discussions about the results obtained.     

Comparison of different mixing phenomena in anaerobic digestion using food waste and sewage treatment plant for green biofuel through simulations of velocity contours

Three-dimensional computational fluid dynamics models have been developed for the comparison of diffuser-based biogas recirculation and impeller mixed anaerobic reactors with unmixed reactors for food waste co-digested with sewage treatment plant sludge for enriched with 60–73% of biogas. Enhanced biogas yield was observed in diffuser mixing, intensity of 2 L/min (0.28–1.180 L/g VSr), compared to impeller mixing of 200 rpm. pH of 5.94 from the feed slurry pH range of 7.0–8.4 shows sheathe-broken microbial SEM structure.     

An Adaptive Neuro-Fuzzy Inference System and Black Widow Optimization Approach for Optimal Resource Utilization and Task Scheduling in a Cloud Environment

Wireless Personal Communications - With the enhancing demand of the cloud computing products, task scheduling issue has become the hot study topic in this area. The task scheduling issue of the...     

Design of Compact D-shaped Frequency Reconfigurable Slot Antenna for Ku/K Band Applications

Wireless Personal Communications - In this paper, a new compact design of frequency reconfigurable slot antenna is presented. The proposed radiating patch consists of two symmetrical D shape slots...     

Biohythane production from organic waste: Recent advancements,technical bottlenecks and prospects

The availability of fossil fuels is a major factor that determines the economy of a country. However, possible exhaustion of fossil fuel deposits as well as increased pollution, and other adverse effects on the environment has prompted us to search for alternative fuels. This resulted in the development of hythane, a blend of hydrogen with methane, at concentrations of 10%–30%. The breakdown of organic substrates using sequential dark fermentation (DF) and anaerobic digestion (AD) leads to biohythane production. The quality and quantity of biohythane can be improved by altering the following aspects: selection, development, and/or genetic engineering of suitable microbial consortium; the use of cheap, appropriate substrates; improved design of bioreactors; and the implementation of two-stage fermentation system. This review focusses on the mechanism of biohythane production and the different aspects involved in increasing both its production rate and quality. A comparative study has also been done to demonstrate the superiority of biohythane over other biofuels.     

Selective peptidic and peptidomimetic inhibitors of Candida albicans myristoylCoA: protein N-myristoyltransferase: a new approach to antifungal therapy

MyristoylCoA: protein N-myristoyltransferase (NMT) catalyzes the cotranslational covalent attachment of a rare cellular fatty acid, myristate, to the N-terminal Gly residue of a variety of eukaryotic proteins. The myristoyl moiety is often essential for expression of the biological functions for these proteins. Attachment of C14:0 alone provides barely enough hydrophobicity to allow stable association with membranes. The partitioning of N-myrisotylproteins is therefore often modulated by "switches" that function through additional covalent or noncovalent modifications. Candida albicans, the principal cause of systemic fungal infection in immunocompromised humans, contains a single NMT gene that is essential for its viability. The functional properties of the acylCoA binding site of human and C. albicans NMT are very similar. However, there are distinct differences in their peptide binding sites. An ADP ribosylation factor (Arf) is included among the few cellular protein substrates of the fungal enzyme. Alanine scanning mutagenesis of an octapeptide derived from an N-terminal Arf sequence (GLYASKLS-NH2) disclosed that Gly1, Ser5, and Lys6 play predominant roles in binding. ALYASKLS-NH2 is an inhibitor competitive for peptide [Ki(app) = 15.3 +/- 6.4 microM] and noncompetitive for myristoylCoA. Remarkably, replacement of the N-terminal tetrapeptide with an 11-aminoundecanoyl group results in a competitive inhibitor (11-aminoundecanoyl-SKLS-NH2) that is approximately 40-fold more potent [Ki(app) = 0.40 +/- 0.03 microM] than the starting octapeptide. Removal of Leu-Ser from the C-terminus generates a competitive dipeptide inhibitor (11-aminoundecanoyl-SK-NH2) with a Ki(app) of 11.7 +/- 0.4 microM, equivalent to that of the starting octapeptide. A derivative dipeptide inhibitor containing a C-terminal N-cyclohexylethyl lysinamide moiety has the advantage of being more potent (IC50 = 0.11 +/- 0.03 microM) and resistant to digestion by cellular carboxypeptidases. Rigidifying the flexible aminoundecanoyl chain results in very potent general NMT inhibitors (IC50 = 40-50 nM). Substituting a 2-methylimidazole for the N-terminal amine and adding a benzylic alpha-methyl group with R stereochemistry to the rigidifying element produces even more potent inhibitors (IC50 = 20-50 nM) that are up to 500-fold selective for the fungal compared to human enzyme. A related less potent member of this series of compounds is fungistatic. Its growth inhibitory effects are associated with a reduction in cellular protein N-myristoylation, judged using cellular Arf as a reporter. These studies establish that NMT is a new antifungal target.