Binding Pattern Determination Of Class of Antifungal Drugs

Crystal Structure of cytochrome p450 2B4 has 476 amino acids, through docking approach we have attempted to explain the specificity of CYP2B4, total 28 imidazole drug were used for the studies as antifungal drugs in which bound bifonazole (reference) shows the binding energy of -8.67 kcal/mol .Compound Miconazole shows the minimum binding energy of -10.45 kcal/mol. The 2B4-bifonazole structure identified 10 residues (ALA 298, GLY 299, GLU 301, THR 302, ILE 363, VAL 292) within 6.5 Å of the active site of bifonazole. GLU 301, THR 302 are also located in 6.5 Å of the bound ligand in 2B4 structure. Due to the presence of the multiple binding substrates in cytochrome p450, it acts as the major target of many drugs in xenobiotic metabolism.
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Structure modeling of RNA using sparse NMR constraints

RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers. Benchmarking on a set of RNAs with complex folds spanning up to 56 nucleotides in length yields structural models that recapitulate experimentally determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 Å. This platform represents an efficient approach for high-throughput RNA structure modeling and will facilitate analysis of diverse, newly discovered functional RNAs

A Structural Model for Vinculin Insertion into PIP 2 -Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization

Vinculin, a scaffolding protein that localizes to focal adhesions (FAs) and adherens junctions, links the actin cytoskeleton to the adhesive super-structure. While vinculin binds to a number of cytoskeletal proteins, it can also associate with phosphatidylinositol 4,5-bisphosphate (PIP2) to drive membrane association. To generate a structural model for PIP2-dependent interaction of vinculin with the lipid bilayer, we conducted lipid-association, nuclear magnetic resonance, and computational modeling experiments. We find that two basic patches on the vinculin tail drive membrane association: the basic collar specifically recognizes PIP2, while the basic ladder drives association with the lipid bilayer. Vinculin mutants with defects in PIP2-dependent liposome association were then expressed in vinculin knockout murine embryonic fibroblasts. Results from these analyses indicate that PIP2 binding is not required for localization of vinculin to FAs or FA strengthening, but is required for vinculin activation and turnover at FAs to promote its association with the force transduction FA nanodomain

RNA Tertiary Structure Analysis by 2′-Hydroxyl Molecular Interference

We introduce a melded chemical and computational approach for probing and modeling higher-order intramolecular tertiary interactions in RNA. 2'-Hydroxyl molecular interference (HMX) identifies nucleotides in highly packed regions of an RNA by exploiting the ability of bulky adducts at the 2'-hydroxyl position to disrupt overall RNA structure. HMX was found to be exceptionally selective for quantitative detection of higher-order and tertiary interactions. When incorporated as experimental constraints in discrete molecular dynamics simulations, HMX information yielded accurate three-dimensional models, emphasizing the power of molecular interference to guide RNA tertiary structure analysis and fold refinement. In the case of a large, multidomain RNA, the Tetrahymena group I intron, HMX identified multiple distinct sets of tertiary structure interaction groups in a single, concise experiment

Last Mile Delivery of Cold Chain Medicines – Challenges and Recommendations

Cold chain medicines are those that require special temperature-controlled cold storage to maintain their quality and efficacy. Cold chain management is important to ensure that the right quality is maintained throughout the supply chain. There lies a variety of reasons why cold chain management continues to be the challenge in India like lack of the consolidated list of cold chain medicines, lack of standard refrigeration guidelines for retail pharmacies, non-uniformity in storage temperature instructions on the label, patient education and lack of awareness. The study aims to identify the challenges faced in the last mile delivery of such medicines in India and suggest practical recommendations for improvement that confirms the international best practices. More than 100 interviews were conducted with healthcare professionals like doctors, pharmacists, retail pharmacy experts, logistic partners, distributors and ex-regulators to understand the storage conditions and the possible solutions, especially at retail and customer level. An exhaustive list of cold chain medicines was framed with the databases of Indian hospitals, local drug distributors and drug retailers. Given the complexity of cold chain system in India, the guidelines for maintaining and managing the cold chain should be clearly available and then be mandatorily followed, in order to avoid the deleterious effects on such medicines due to storage and handling issues as elaborated in this study

Deep Sequencing Identification of Novel Glucocorticoid-Responsive miRNAs in Apoptotic Primary Lymphocytes

<div><p>Apoptosis of lymphocytes governs the response of the immune system to environmental stress and toxic insult. Signaling through the ubiquitously expressed glucocorticoid receptor, stress-induced glucocorticoid hormones induce apoptosis via mechanisms requiring altered gene expression. Several reports have detailed the changes in gene expression mediating glucocorticoid-induced apoptosis of lymphocytes. However, few studies have examined the role of non-coding miRNAs in this essential physiological process. Previously, using hybridization-based gene expression analysis and deep sequencing of small RNAs, we described the prevalent post-transcriptional repression of annotated miRNAs during glucocorticoid-induced apoptosis of lymphocytes. Here, we describe the development of a customized bioinformatics pipeline that facilitates the deep sequencing-mediated discovery of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. This analysis identifies the potential presence of over 200 novel glucocorticoid-responsive miRNAs. We have validated the expression of two novel glucocorticoid-responsive miRNAs using small RNA-specific qPCR. Furthermore, through the use of Ingenuity Pathways Analysis (IPA) we determined that the putative targets of these novel validated miRNAs are predicted to regulate cell death processes. These findings identify two and predict the presence of additional novel glucocorticoid-responsive miRNAs in the rat transcriptome, suggesting a potential role for both annotated and novel miRNAs in glucocorticoid-induced apoptosis of lymphocytes.</p> </div

RNA Tertiary Structure Analysis by 2′-Hydroxyl Molecular Interference

We introduce a melded chemical and computational approach for probing and modeling higher-order intramolecular tertiary interactions in RNA. 2′-Hydroxyl molecular interference (HMX) identifies nucleotides in highly packed regions of an RNA by exploiting the ability of bulky adducts at the 2′-hydroxyl position to disrupt overall RNA structure. HMX was found to be exceptionally selective for quantitative detection of higher-order and tertiary interactions. When incorporated as experimental constraints in discrete molecular dynamics simulations, HMX information yielded accurate three-dimensional models, emphasizing the power of molecular interference to guide RNA tertiary structure analysis and fold refinement. In the case of a large, multidomain RNA, the <i>Tetrahymena</i> group I intron, HMX identified multiple distinct sets of tertiary structure interaction groups in a single, concise experiment

Pathways analysis predicts novel miRNA targets may contribute to glucocorticoid-induced apoptosis.

<div><p>(A) miRNA target predictions for novel miRNA candidates 44 and 166 were performed using the miRanda miRNA target prediction algorithm. The number of target mRNAs differentially expressed during glucocorticoid-induced apoptosis (p < 0.01; fold change > 1.2) is indicated for each candidate. </p> <p>(B) IPA-generated ranking of the top five molecular and cellular functions of genes differentially expressed during glucocorticoid-induced apoptosis (p < 0.01; fold change > 1.2), as well as the predicted targets of both candidates 44 and 166 (p-values for top functions are indicated beneath each ranking). Genes differentially expressed during glucocorticoid-induced apoptosis were identified by whole genome microarray analysis of untreated and 100nM dexamethasone-treated thymocytes (6 hours, 3 biological replicates). </p> <p>(C) Venn diagram analysis identified specific novel candidate predicted targets differentially expressed during glucocorticoid-induced apoptosis (p<.01) and the application IPA to this combined gene list (40 genes) generated a top 5 ranking of molecular and cellular functions regulated by these predicted targets (p-values for top functions are indicated beneath each ranking). </p></div