Homology Model-Based Virtual Screening for the Identification of Human Helicase DDX3 Inhibitors

Targeting cellular cofactors instead of viral enzymes represents a new strategy to combat infectious diseases, which should help to overcome the problem of viral resistance. Recently, it has been revealed that the cellular ATPase/RNA helicase X-linked DEAD-box polypeptide 3 (DDX3) is an essential host factor for the replication of several viruses such as HIV, HCV, JEV, Dengue, and West Nile. Accordingly, a drug targeting DDX3 could theoretically inhibit all viruses that are dependent on this host factor. Herein, for the first time, a model of hDDX3 in its closed conformation, which binds the viral RNA was developed by using the homology module of Prime through the Maestro interface of Schrodinger. Next, a structure-based virtual screening protocol was applied to identify DDX3 small molecule inhibitors targeting the RNA binding pocket. As a result, an impressive hit rate of 40% was obtained with the identification of 10 active compounds out of the 25 tested small molecules. The best poses of the active ligands highlighted the crucial residues to be targeted for the inhibition of the helicase activity of DDX3. The obtained results confirm the reliability of the constructed DDX3/RNA model and the proposed computational strategy for investigating novel DDX3 inhibitors.

Diamine Functionalized Cubic Mesoporous Silica for Ibuprofen Controlled Delivery

A diamine functionalized cubic mesostructured KIT-6 (N-KIT-6) has been prepared by post-synthetic method using calcined mesoporous KIT-6 with a diamine source, i.e., N-'[3-(tri methoxysilyl)- propyl]'ethylenediamine. The KIT-6 mesoporous silica used for N-KIT-6 was synthesized under weak acidic hydrothermal method using bitemplates, viz., Pluronic P123 and 1-butanol. The synthesized mesoporous materials, KIT-6 and N-KIT-6, have been characterized by the relevant instrumental techniques such as SAXS, N2 sorption isotherm, FT-IR, SEM, TEM and TGA to prove the standard mesoporous materials with the identification of diamine groups. The characterized mesoporous materials, KIT-6 and N-KIT-6, have been extensively used in the potential application of controlled drug delivery, where ibuprofen (IBU) employed as a model drug. The rate of IBU adsorption and release was monitored by UV vis-spectrometer. On the basis of the experimental results of controlled drug delivery system, the results of IBU adsorption and releasing rate in N-KIT-6 are higher than those of KIT-6 because of the higher hydrophobic nature as well as rich basic sites on the surface of inner pore wall silica.

Metabolomics and partial least square discriminant analysis to predict history of myocardial infarction of self-claimed healthy subjects: validity and feasibility for clinical practice

Background

The dynamics of metabolomics in establishing a prediction model using partial least square discriminant analysis have enabled better disease diagnosis; with emphasis on early detection of diseases. We attempted to translate the metabolomics model to predict the health status of the Orang Asli community whom we have little information. The metabolite expressions of the healthy vs. diseased patients (cardiovascular) were compared. A metabotype model was developed and validated using partial least square discriminant analysis (PLSDA). Cardiovascular risks of the Orang Asli were predicted and confirmed by biochemistry profiles conducted concurrently.

Results

Fourteen (14) metabolites were determined as potential biomarkers for cardiovascular risks with receiver operating characteristic of more than 0.7. They include 15S-HETE (AUC = 0.997) and phosphorylcholine (AUC = 0.995). Seven Orang Asli were clustered with the patients’ group and may have ongoing cardiovascular risks and problems. This is supported by biochemistry tests results that showed abnormalities in cholesterol, triglyceride, HDL and LDL levels.

Conclusions

The disease prediction model based on metabolites is a useful diagnostic alternative as compared to the current single biomarker assays. The former is believed to be more cost effective since a single sample run is able to provide a more comprehensive disease profile, whilst the latter require different types of sampling tubes and blood volumes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13336-015-0018-4) contains supplementary material, which is available to authorized users.

Nodamura virus B2 amino terminal domain sensitivity to small interfering RNA

Nodamura virus (NoV) B2, a suppressor of RNA interference, binds double stranded RNAs (dsRNAs) and small interfering RNAs (siRNAs) corresponding to Dicer substrates and products. Here, we report that the amino terminal domain of NoV B2 (NoV B2 79) specifically binds siRNAs but not dsRNAs. NoV B2 79 oligomerizes on binding to 27 nucleotide siRNA. Mutation of the residues phenylalanine49 and alanine60 to cysteine and methionine, respectively enhances the RNA binding affinity of NoV B2 79. Circular dichroism spectra demonstrated that the wild type and mutant NoV B2 79 have similar secondary structure conformations.

Cyclic ligand functionalized mesoporous silica (SBA-15) for selective adsorption of Co2+ ion from artificial seawater

Hard donor atoms (N and O) containing macrocyclic ligand was synthesized and further functionalized with mesoporous SBA-15 materials by chemical modification method. The modification was achieved by the immobilization of 3-chloropropyltriethoxysilane (CIPTES) onto mesoporous silica surface followed by post grafting route. The resulting material (Py-Cy-SBA-15) has been characterized by low angle X-ray diffraction (XRD), nitrogen adsorption-desorption isotherm, Fourier-transform infrared (FT-IR) spectroscopy, 29Si and 13C CP MAS NMR spectroscopic analyses, Thermogravimetric analysis (TGA) and elemental analysis. The long range orders of the materials were identified by transmission electron microscopy (TEM). The functionalized material was employed to the heavy metal ions adsorption from aqueous solution containing Cu2+, Co2+, Zn2+, Cd2+ and Cr2+. The prepared hybrid material showed high selectivity and adsorption capacity for Co2+ ion at pH 8.0.

Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants

Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action. Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the presence of E. coli EF-G alone). Crystal structure had revealed higher rigidity of the M. tuberculosis RRF due to the presence of additional salt bridges between domains. Two inter-domain salt bridges and one between the linker region and the domain containing C-terminal residues were disrupted by appropriate mutations. Except for a C-terminal deletion mutant, all mutants showed RRF activity in E. coli when M. tuberculosis EF-G was also co-expressed. The crystal structures of the point mutants, that of the C-terminal deletion mutant and that of the protein grown in the presence of a detergent, were determined. The increased mobility resulting from the disruption of the salt bridge involving the hinge region allows the appropriate mutant to weakly complement E. coli for its deficiency of RRF even in the absence of simultaneous expression of the mycobacterial EF-G. The loss of activity of the C-terminal deletion mutant appears to be partly due to the rigidification of the molecule consequent to changes in the hinge region.

Selective oxidation of cyclohexane using Ce1-xMnxO2 nanocatalysts

The Ce1-xMnxO2 nanocatalysts (x = 0.25, 0.50 and 0.75 wt.%) were synthesized by sol-gel method. The catalysts were characterized using various techniques such as XRD, N2 sorption study, DRSUV-Vis, TPR, SEM and TEM. The incorporation of Mn ions into the ceria lattice was confirmed by XRD analysis. DRUV-Vis spectra confirm the presence of Ce3+ ions in the lattice of Ce1-xMnxO2. H2-TPR study revealed the oxygen storage capacity of the catalyst. The 3D flowerlike morphology of the nanocatalysts was confirmed from FESEM and HRTEM images. The catalytic activity was tested for the vapor phase oxidation of cyclohexane using air as an oxidant. The key reaction parameters were varied to study the stability, activity and selectivity of the catalysts. The study concluded that suitable amount of manganese content is essential for the selective oxidation of cyclohexane at low temperature and Ce0.25Mn0.75O2 is the most suitable catalyst for high conversion and selectivity under the given reaction conditions. The activity of the catalyst is correlated with the characterization results.

Incessant formation of chain-like mesoporous silica with a superior binding capacity for mercury

A new chain type mesoporous silica has been easily synthesized to remove mercury ions from an aqueous medium.

Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule

The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M. tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

Cloning, expression, purification, crystallization and preliminary X-ray studies of a secreted lectin (Rv1419) from Mycobacterium tuberculosis

A secreted lectin, Rv1419, from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized and the crystals have been characterized. This represents the first X-ray investigation of a lectin or lectin-like molecule from the pathogen. The cubic crystals contain one molecule in the asymmetric unit. Sequence comparisons indicate that the lectin has a β-trefoil fold and belongs to a well characterized family of carbohydrate-binding modules. Structural analysis of the crystals is in progress.

Expression of SEAP (secreted alkaline phosphatase) by baculovirus mediated transduction of HEK 293 cells in a hollow fiber bioreactor system

A BacMam baculovirus was designed in our laboratory to express the reporter protein secreted alkaline phosphatase (SEAP) driven by the immediate early promoter of human cytomegalovirus promoter (CMV). In vitro tests have been carried out using this recombinant baculovirus to study the secreted protein in two cell lines and under various culture conditions. The transductions were carried out on two commonly used mammalian cell lines namely the human embryonic kidney (HEK 293A) and Chinese hamster ovary (CHO-K1). Initial studies clearly demonstrated that the transient expression of SEAP was at least 10-fold higher in the HEK 293 cells than the CHO cells under equivalent experimental conditions. Factorial design experiments were done to study the effect of different parameters such as cell density, MOI, and the histone deacetylase inhibitor, trichostatin A concentration. The multiplicity of infection (MOI) and the cell density were found to have the most impact on the process. The enhancer trichostatin A also showed some positive effect. The production of secreted protein in a batch reactor was studied using the Wave disposable bioreactor system. A semi-continuous perfusion process was developed to extend the period of gene expression in mammalian cells using a hollow fiber bioreactor system (HFBR). The growth of cells and viability in both systems was monitored by offline analyses of metabolites. The expression of recombinant protein could be maintained over an extended period of time up to 30 days in the HFBR.

Structural plasticity and enzyme action: crystal structures of mycobacterium tuberculosis peptidyl-tRNA hydrolase

Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis. The structure of the enzyme from Mycobacterium tuberculosis has been determined in three crystal forms. This structure and the structure of the enzyme from Escherichia coli in its crystal differ substantially on account of the binding of the C terminus of the E. coli enzyme to the peptide-binding site of a neighboring molecule in the crystal. A detailed examination of this difference led to an elucidation of the plasticity of the binding site of the enzyme. The peptide-binding site of the enzyme is a cleft between the body of the molecule and a polypeptide stretch involving a loop and a helix. This stretch is in the open conformation when the enzyme is in the free state as in the crystals of M. tuberculosis peptidyl-tRNA hydrolase. Furthermore, there is no physical continuity between the tRNA and the peptide-binding sites. The molecule in the E. coli crystal mimics the peptide-bound enzyme molecule. The peptide stretch referred to earlier now closes on the bound peptide. Concurrently, a channel connecting the tRNA and the peptide-binding site opens primarily through the concerted movement of two residues. Thus, the crystal structure of M. tuberculosis peptidyl-tRNA hydrolase when compared with the crystal structure of the E. coli enzyme, leads to a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule.

X-ray studies of crystalline complexes involving amino acids and peptides. XLIV. Invariant features of supramolecular association and chiral effects in the complexes of arginine and lysine with tartaric acid

The tartaric acid complexes with arginine and lysine exhibit two stoichiometries depending upon the ionization state of the anion. The structures reported here are DL-argininium DL-hydrogen tartrate, bis(L-argininium) L-tartrate, bis(DL-lysinium) DL-tartrate monohydrate, L-lysinium D-hydrogen tartrate and L-lysinium L-hydrogen tartrate. During crystallization, L-lysine preferentially interacts with D-tartaric acid to form a complex when DL-tartaric acid is used in the experiment. The anions and the cations aggregate into separate alternating layers in four of the five complexes. In bis(L-argininium) L-tartrate, the amino acid layers are interconnected by individual tartrate ions which do not interact among themselves. The aggregation of argininium ions in the DL- and the L-arginine complexes is remarkably similar, which is in turn similar to those observed in other dicarboxylic acid complexes of arginine. Thus, argininium ions have a tendency to assume similar patterns of aggregation, which are largely unaffected by a change in the chemistry of partner molecules such as the introduction of hydroxyl groups or a change in chirality or stoichiometry. On the contrary, the lysinium ions exhibit fundamentally different aggregation patterns in the DL–DL complexes on the one hand and L–D and L–L complexes on the other. Interestingly, the pattern in the L–D complex is similar to that in the L–L complex. The lysinium ions in the DL–DL complex exhibit an aggregation pattern similar to those observed in the DL-lysine complexes involving other dicarboxylic acids. Thus, the effect of change in the chirality of a subset of the component complexes could be profound or marginal, in an unpredictable manner. The relevant crystal structures appear to indicate that the preference of L-lysine for D-tartaric acid is perhaps caused by chiral discrimination resulting from the amplification of a small energy difference.

Direct Synthesis of Well-Ordered and Unusually Reactive MnSBA-15 Mesoporous Molecular Sieves with High Manganese Content

The mesoporous MnSBA-15 materials with different n(Si)/n(Mn) ratios of 4, 8, 20, and 50 have been synthesized, for the first time, using manganese nitrate tetrahydrate and Pluronic 123 triblock polymer [(EO)20(PO)70(EO)20] by simply adjusting the molar ratio of water to hydrochloric acid (n(H2O)/n(HCl)) under direct hydrothermal conditions. For the effect of structural and textural properties with incorporation of manganese, the MnSBA-15 has been synthesized with different synthesis temperatures at the fixed molar ratios of n(Si)/n(Mn) = 4 and n(H2O)/n(HCl) = 295 in the synthesis gel. The hydrothermal and thermal stabilities of MnSBA-15 have also been investigated. The calcined MnSBA-15 materials prepared have been characterized by ICP-AES, XRD, N2 adsorption, ESR, FE-SEM, and TEM. The ICP-AES studies show a higher amount of manganese incorporation on the silica pore walls, as MnSBA-15 with a n(Si)/n(Mn) ratio up to 2.2 can be successfully prepared at a fixed n(H2O)/n(HCl) molar ratio of 295 by adjusting the ratios of n(Si)/n(Mn) in the synthesis gel. The structural and textural properties of calcined MnSBA-15 prepared can be found by the results of XRD and N2 adsorption. The investigation of ESR results clearly describe the effect of structure and Mn species coordination on the SBA-15 silica pore walls while the uniform pore diameter and rope-like hexagonal mesoporous structure of MnSBA-15 can be identified by TEM and FE-SEM images. With increasing synthesis temperature, an increase the unit cell parameter, pore size, and pore volume and a decrease the specific surface area and pore wall thickness of MnSBA-15 can be obviously noted by the results of XRD and N2 adsorption. The hexagonal MnSBA-15 materials prepared could be tested as catalysts in epoxidation of trans-stilbene to produce trans-stilbene oxide under various optimal conditions while their catalytic properties could also be compared to the results of MnMCM-41 and ZrMnMCM-41.

Cloning, expression, purification, crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis

Peptidyl-tRNA hydrolase catalyses the cleavage of the ester link between the peptide and the tRNA in peptidyl-tRNAs that, for various reasons, have dropped off the translating ribosomes. This enzyme from Mycobacterium tuberculosis has been crystallized in three related but distinct forms: P2(1)2(1)2(1), unit-cell parameters a = 36.30, b = 61.85, c = 73.97 A, P2(1), a = 35.83, b = 73.79, c = 59.79 A, beta = 92.3 degrees , and P2(1)2(1)2(1), a = 35.84, b = 57.06, c = 72.59 A. X-ray data have been collected from all three forms.

Effect of short-term treatment of eugenol on the seminal vesicles of adult albino rats

The structure and biochemical content of adult albino rat seminal vesicles, were studied, after administration of two different doses of eugenol for 10 days (0.2 and 0.3 mg/kg/day, i.m.). Marked decreases in the concentrations of nucleic acids, fructose and total protein as well as RNA/DNA ratio (61%) and protein/DNA ratio (27%) were observed. A remarkable increase in phospholipid concentration was noted with a corresponding decrease in neutral lipids. Histologically, eugenol treated animals showed degeneration of the secretory columnar cells and well developed myofibrillar connective tissues when compared to control animals.