Structural Studies Of Analgesics And Their Interactions .1. Crystal And Molecular-Structure Of Antipyrine

The complex crystallizes in the space group P21/c with four formula units in a unit cell of dimensionsa= 12.747, b= 7.416, c= 17.894 A and/3= 90.2 °. The structure has been solved by the symbolic addition procedure using three dimensional photographic data and refined to an R value of 0.079 for 2019 observed reflexions. The pyramidal nature of the two hetero nitrogen atoms in the antipyrine molecule is inter:nediate between that observed in free antipyrine and in some of its metal complexes. The molecule is more polar than that in crystals of free antipyrine but less so compared with that in metal complexes. In the salicylic acid molecule, the hydroxyl group forms an internal hydrogen bond with one of the oxygen atoms in the carboxyl group. The association between the salicylic acid and the antipyrine molecules is achieved through an intermolecular hydrogen bond with the other carboxyl oxygen atom in the salicylic acid molecule as the proton donor and the carboxyl oxygen atom of the antipyrine molecule as the acceptor

Molecular Complexes of Alprazolam with Carboxylic Acids, Boric Acid, Boronic Acids, and Phenols. Evaluation of Supramolecular Heterosynthons Mediated by a Triazole Ring

A series of molecular complexes, both co-crystals and salts, of a triazole drug-alprazolam-with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O-H center dot center dot center dot N hydrogen bonds with the triazole ring. (C) 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3743-3753, 2010.

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

Differences in hydration and association of helical Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-(Val-Ala-Leu-Aib)2-OMe. xH2O in two crystalline polymorphs

The 15-residue apolar peptide, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-(Val-Ala-Leu-Aib)h2a-sO Mebeen crystallized from 2-propanol-water (form I). The crystal parameters for I are as follows:C74H133N15018*2H20s,p ace group P21, a = 9.185 (6) A, b = 47.410 (3) A, c = 10.325 (9) A, @ = 91.47(2)O, 2 = 2, R = 6.3% for 4532 reflections observed >3aQ, resolution 0.94 A. The structure isalmost completely a-helical with eleven 5-1 hydrogen bonds and one 441 hydrogen bond nearthe N-terminus. The structure has been compared with a polymorph (form 11) obtained frommethanol-water (Karle, I. L.; Flippen-Anderson, J. L.; Uma, K.; Sukumar, M.; Balaram, P., J. An.Chem. SOC19. 90,112,9350-9356). The two forms differ in the extent of hydration; form I contains two water molecules in the head-to-tail region of helical columns, while form I1 is more extensively solvated, with the equivalent of 7.5 water molecules. The three-dimensional packing of helices is completely parallel in I and antiparallel in 11.

Bile acid based semi-rigid molecular tweezers

The easily constructed bile acid-based semi-rigid molecular tweezer 2 binds guest 8 in chloroform with an association constant of 83 dm(3) mol(-1).

Diacetylenic lipid tubules:experimental evidence for a chiral molecular architecture

Molecular self-assembly is of key importance for the rational design of advanced materials. To investigate the causal relation between molecular structure and the consequent self-assembled microstructure, self-assembled tubules of diacetylenic lipids were studied. Circular-dichroism studies give experimental evidence that the formation of tubules is driven by chiral molecular packing, in agreement with recent theories of tubules. On the basis of these results, a molecular mechanism for the formation of tubules is proposed.

High Rydberg state carbon recombination lines toward Cassiopeia A: 332 MHz VLA observations and comparison with H I and molecular lines

We present observations of the C270alpha carbon recombination line, 21 cm neutral hydrogen line and (CO)-C-12 (J = 1 --> 0) molecular line toward Cas A. A comparison of the distribution of recombination line optical depths over the face of Cas A with that of H I optical depths and molecular line emission favors the association of C270alpha regions with H I rather than molecular clouds. The association makes it possible to self-consistently determine several physical parameters of the clouds by combining the recombination line and 21 cm H I measurements.

Design, synthesis, and evaluation of bile acid-based molecular tweezers

A family of bile acid-based molecular tweezers (7-9) has been constructed readily from simple precursors. Binding experiments with various electron deficient aromatic compounds showed that tweezer 8 binds trinitrofluorenone 10e with an association constant of 220 M(-1) in CDCl3. Single-crystal X-ray analysis of compound 8 shows aromatic-aromatic interactions producing a two-dimensional lattice of pyrene units. Tweezer 8 was immobilized on Merrifield resin, and binding studies have shown that these data compare well with those of the solution state studies.

Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1 alpha and PKR

Background: Interaction of non-structural protein 5A (NS5A) of Hepatitis C virus (HCV) with human kinases namely, casein kinase 1 alpha (ck1 alpha) and protein kinase R (PKR) have different functional implications such as regulation of viral replication and evasion of interferon induced immune response respectively. Understanding the structural and molecular basis of interactions of the viral protein with two different human kinases can be useful in developing strategies for treatment against HCV. Results: Serine 232 of NS5A is known to be phosphorylated by human ck1 alpha. A structural model of NS5A peptide containing phosphoacceptor residue Serine 232 bound to ck1 alpha has been generated using the known 3-D structures of kinase-peptide complexes. The substrate interacting residues in ck1 alpha has been identified from the model and these are found to be conserved well in the ck1 family. ck1 alpha - substrate peptide complex has also been used to understand the structural basis of association between ck1 alpha and its other viral stress induced substrate, tumour suppressor p53 transactivation domain which has a crystal structure available. Interaction of NS5A with another human kinase PKR is primarily genotype specific. NS5A from genotype 1b has been shown to interact and inhibit PKR whereas NS5A from genotype 2a/3a are unable to bind and inhibit PKR efficiently. This is one of the main reasons for the varied response to interferon therapy in HCV patients across different genotypes. Using PKR crystal structure, sequence alignment and evolutionary trace analysis some of the critical residues responsible for the interaction of NS5A 1b with PKR have been identified. Conclusions: The substrate interacting residues in ck1 alpha have been identified using the structural model of kinase substrate peptide. The PKR interacting NS5A 1b residues have also been predicted using PKR crystal structure, NS5A sequence analysis along with known experimental results. Functional significance and nature of interaction of interferon sensitivity determining region and variable region 3 of NS5A in different genotypes with PKR which was experimentally shown are also supported by the findings of evolutionary trace analysis. Designing inhibitors to prevent this interaction could enable the HCV genotype 1 infected patients respond well to interferon therapy.

Hybrid organogels and aerogels from co-assembly of structurally different low molecular weight gelators

The blending of perfluorinated bile ester derivatives with the gelator 2,3-didecyloxyanthracene (DDOA) yields a new class of hybrid organo- and aerogels displaying a combination of optical and mechanical properties that differ from those of pure gels. Indeed, the nanofibers constituting the hybrid organogels emit polarized blue light and display dichroic near-UV absorption via the achiral DDOA molecules, thanks to their association with a chiral bile ester. Moreover, the thermal stability and the mechanical yield stress of the mixed organogels in DMSO are enhanced for blends of DDOA with the deoxycholic gelator (DC11) having a C-11 chain, as compared to the pure components' gels. When the chain length of the ester is increased to C-13 (DC13) a novel compound for aerogel formation directly in scCO(2) is obtained under the studied conditions. A mixture of this compound with DDOA is also able to gelate scCO(2) leading to novel composite aerogel materials. As revealed by SAXS measurements, the hybrid and the pure DDOA and DC13 aerogels display cell parameters that are very similar. These SAXS experiments suggest that crystallographic conditions are very favorable for the growth of hybrid molecular arrangements in which DDOA and DC13 units could be interchanged. Specific molecular interactions between two components are not always a pre-requisite condition for the formation of a hybrid nanostructured material in which the components mutually induce properties.

Fourteen gene GBM prognostic signature identifies association of immune response pathway and mesenchymal subtype with high risk group

Background: Recent research on glioblastoma (GBM) has focused on deducing gene signatures predicting prognosis. The present study evaluated the mRNA expression of selected genes and correlated with outcome to arrive at a prognostic gene signature. Methods: Patients with GBM (n = 123) were prospectively recruited, treated with a uniform protocol and followed up. Expression of 175 genes in GBM tissue was determined using qRT-PCR. A supervised principal component analysis followed by derivation of gene signature was performed. Independent validation of the signature was done using TCGA data. Gene Ontology and KEGG pathway analysis was carried out among patients from TCGA cohort. Results: A 14 gene signature was identified that predicted outcome in GBM. A weighted gene (WG) score was found to be an independent predictor of survival in multivariate analysis in the present cohort (HR = 2.507; B = 0.919; p < 0.001) and in TCGA cohort. Risk stratification by standardized WG score classified patients into low and high risk predicting survival both in our cohort (p = <0.001) and TCGA cohort (p = 0.001). Pathway analysis using the most differentially regulated genes (n = 76) between the low and high risk groups revealed association of activated inflammatory/immune response pathways and mesenchymal subtype in the high risk group. Conclusion: We have identified a 14 gene expression signature that can predict survival in GBM patients. A network analysis revealed activation of inflammatory response pathway specifically in high risk group. These findings may have implications in understanding of gliomagenesis, development of targeted therapies and selection of high risk cancer patients for alternate adjuvant therapies.

Analysis of designed beta-hairpin peptides: molecular conformation and packing in crystals

The crystal structures of several designed peptide hairpins have been determined in order to establish features of molecular conformations and modes of aggregation in the crystals. Hairpin formation has been induced using a centrally positioned (D)Pro-Xxx segment (Xxx = (L)Pro, Aib, Ac(6)c, Ala; Aib = alpha-aminoisobutyric acid; Ac(6)c = 1-aminocyclohexane-1-carboxylic acid). Structures of the peptides Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1), Boc-Leu-Tyr-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (2, polymorphic forms labeled as 2a and 2b), Boc-Leu-Val-Val-(D)Pro-(L)Pro-Leu-Val-Val-OMe (3), Boc-Leu-Phe-Val-(D)Pro-Aib-Leu-Phe-Val-OMe (4, polymorphic forms labeled as 4a and 4b), Boc-Leu-Phe-Val-(D)Pro-Ac(6)c-Leu-Phe-Val-OMe (5) and Boc-Leu-Phe-Val-(D)Pro-Ala-Leu-Phe-Val-OMe (6) are described. All the octapeptides adopt type II' beta-turn nucleated hairpins, stabilized by three or four cross-strand intramolecular hydrogen bonds. The angle of twist between the two antiparallel strands lies in the range of -9.8 degrees to -26.7 degrees. A detailed analysis of packing motifs in peptide hairpin crystals is presented, revealing three broad modes of association: parallel packing, antiparallel packing and orthogonal packing. An attempt to correlate aggregation modes in solution with observed packing motifs in crystals has been made by indexing of crystal faces in the case of three of the peptide hairpins. The observed modes of hairpin aggregation may be of relevance in modeling multiple modes of association, which may provide insights into the structure of insoluble polypeptide aggregates.

Regulation of protumorigenic pathways by Insulin like growth factor binding protein2 and its association along with beta-catenin in breast cancer lymph node metastasis

Background: Insulin like growth factor binding proteins modulate the mitogenic and pro survival effects of IGF. Elevated expression of IGFBP2 is associated with progression of tumors that include prostate, ovarian, glioma among others. Though implicated in the progression of breast cancer, the molecular mechanisms involved in IGFBP2 actions are not well defined. This study investigates the molecular targets and biological pathways targeted by IGFBP2 in breast cancer. Methods: Transcriptome analysis of breast tumor cells (BT474) with stable knockdown of IGFBP2 and breast tumors having differential expression of IGFBP2 by immunohistochemistry was performed using microarray. Differential gene expression was established using R-Bioconductor package. For validation, gene expression was determined by qPCR. Inhibitors of IGF1R and integrin pathway were utilized to study the mechanism of regulation of beta-catenin. Immunohistochemical and immunocytochemical staining was performed on breast tumors and experimental cells, respectively for beta-catenin and IGFBP2 expression. Results: Knockdown of IGFBP2 resulted in differential expression of 2067 up regulated and 2002 down regulated genes in breast cancer cells. Down regulated genes principally belong to cell cycle, DNA replication, repair, p53 signaling, oxidative phosphorylation, Wnt signaling. Whole genome expression analysis of breast tumors with or without IGFBP2 expression indicated changes in genes belonging to Focal adhesion, Map kinase and Wnt signaling pathways. Interestingly, IGFBP2 knockdown clones showed reduced expression of beta-catenin compared to control cells which was restored upon IGFBP2 re-expression. The regulation of beta-catenin by IGFBP2 was found to be IGF1R and integrin pathway dependent. Furthermore, IGFBP2 and beta-catenin are co-ordinately overexpressed in breast tumors and correlate with lymph node metastasis. Conclusion: This study highlights regulation of beta-catenin by IGFBP2 in breast cancer cells and most importantly, combined expression of IGFBP2 and beta-catenin is associated with lymph node metastasis of breast tumors.

Non-polio enteroviruses and their association with acute diarrhea in children in India

A causative agent in approximately 40% of diarrhea] cases. still remains unidentified. Though many enteroviruses (EVs) are transmitted through fecal-oral route and replicate in the intestinal cells, their association with acute diarrhea has not so far been recognized due to lack of detailed epidemiological investigations. This long-term, detailed molecular epidemiological study aims to conclusively determine the association of non-polio enteroviruses (NPEVs) with acute diarrhea in comaparison with rotavirus (RV) in children. Diarrheal stool specimens from 2161 children aged 0-2 years and 169 children between 2 and 9 years, and 1800 normal stool samples from age-matched healthy children between 0 and 9 years were examined during 2008-2012 for enterovirus (oral polio vaccine strains (OPVs) and NPEVs). Enterovirus serotypes were identified by complete VP1 gene sequence analysis. Enterovirus and rotavirus were detected in 19.01% (380/2330) and 13.82% (322/2330) diarrheal stools. During the study period, annual prevalence of EV- and RV-associated diarrhea ranged between 8% and 22%, but with contrasting seasonal prevalence with RV predominating during winter months and NPEV prevailing in other seasons. NPEVs are associated with epidemics-like outbreaks during which they are detected in up to 50% of diarrheic children, and in non-epidemic seasons in 0-10% of the patients. After subtraction of OPV-positive diarrheal cases (1.81%), while NPEVs are associated with about 17% of acute diarrhea, about 6% of healthy children showed asymptomatic NPEV excretion. Of 37 NPEV serotypes detected in diarrheal children, seven echovirus types 1, 7, 11, 13, 14, 30 and 33 are frequently observed, with Ell being more prevalent followed by E30. In conclusion, NPEVs are significantly associated with acute diarrhea, and NPEVs and rotavirus exhibit contrasting seasonal predominance. This study signifies the need for a new direction of research on enteroviruses involving systematic analysis of their contribution to diarrheal burden. (C) 2013 Elsevier B.V. All rights reserved.