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Int. J. Mol. Sci., Volume 8, Issue 2 (February 2007), Pages 70-179

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Research

Open AccessArticle Microwave-Assisted Synthesis of Phenothiazine and Qinoline Derivatives
Int. J. Mol. Sci. 2007, 8(2), 70-80; doi:10.3390/i8020070
Received: 27 October 2006 / Accepted: 12 February 2007 / Published: 13 February 2007
Cited by 22 | PDF Full-text (85 KB) | HTML Full-text | XML Full-text
Abstract
Application of a dynamic microwave power system in the chemical synthesis ofsome phenothiazine and quinoline derivatives is described. Heterocyclic ring formation,aromatic nucleophilic substitution and heterocyclic aldehydes/ketones condensationreactions were performed on solid support, or under solvent free reaction conditions. Themicrowave-assisted Duff formylation of [...] Read more.
Application of a dynamic microwave power system in the chemical synthesis ofsome phenothiazine and quinoline derivatives is described. Heterocyclic ring formation,aromatic nucleophilic substitution and heterocyclic aldehydes/ketones condensationreactions were performed on solid support, or under solvent free reaction conditions. Themicrowave-assisted Duff formylation of phenothiazine was achieved. Comparison ofmicrowave-assisted synthesis with the conventional synthetic methods demonstratesadvantages related to shorter reaction times and in some cases better reaction yields. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Efficient Gene Transfection into Mammalian Cells Mediated by Cross-linked Polyethylenimine
Int. J. Mol. Sci. 2007, 8(2), 81-102; doi:10.3390/i8020081
Received: 15 December 2006 / Accepted: 31 January 2007 / Published: 14 February 2007
Cited by 7 | PDF Full-text (2490 KB) | HTML Full-text | XML Full-text
Abstract
25 kDa branched polyethylenimine (PEI) has successfully been used for in vitroand in vivo gene delivery approaches, but it is cytotoxic. Smaller PEIs are usually non-cytotoxic but less efficient. In order to enhance the gene delivery efficiency and minimizecytotoxicity of PEI, we [...] Read more.
25 kDa branched polyethylenimine (PEI) has successfully been used for in vitroand in vivo gene delivery approaches, but it is cytotoxic. Smaller PEIs are usually non-cytotoxic but less efficient. In order to enhance the gene delivery efficiency and minimizecytotoxicity of PEI, we explored to synthesize cross-linked PEIs with degradable bonds byreacting amines of small branched 2000 Da PEI with small diacrylate (1,4-butanedioldiacrylate or ethyleneglycol dimethacrylate) for 2-6 hours. The efficiency of the cross-linkedPEIs during in vitro delivering plasmid containing enhanced green fluorescent protein(EGFP) gene reporter and their cytotoxicity were assessed in melanoma B16F10 cell andother cell lines. In vivo gene delivery efficiency was evaluated by direct injection delivery ofthe EGFP plasmid/ cross-linked PEI complexes into mice and by estimating the EGFPexpression in animal muscles. Compared to commercially available 25-kDa branched PEI,the cross-linked PEIs reported here could mediate more efficient expression of reporter genethan the 25-kDa PEI control, 19-fold more efficiently in B16F10 cells, 17-fold in 293T cells, 2.3-fold in 3T3 cells, and they exhibited essentially nontoxic at their optimized condition for gene delivery. Furthermore the transfection activity of polyplexs was preserved in the presence of serum proteins. The muscle transfected with the cross-linked PEI prepared here exhibited normal morphology and excellent gene expression. The cross-linked PEIs reported here were evidently more efficient than the commercial 25-kD PEI control and had less cytotoxicity in gene delivery in vitro and in vivo. Full article
(This article belongs to the Special Issue Interaction of Biological Molecules)
Open AccessArticle Electron Charge Density Distribution from X-ray Diffraction Study of the M-Nitrophenol Compound in the Monoclinic Form
Int. J. Mol. Sci. 2007, 8(2), 103-115; doi:10.3390/i8020103
Received: 30 October 2006 / Accepted: 17 January 2007 / Published: 16 February 2007
Cited by 4 | PDF Full-text (190 KB) | HTML Full-text | XML Full-text
Abstract
At room temperature, the m-Nitrophenol (m-NPH) appears in two polymorphicstructures: orthorhombic and monoclinic forms. In the present work, we shall focus on themonoclinic form of this compound which has a centrosymmetric structure with the spacegroup P21/n. The molecular dipole moment has been [...] Read more.
At room temperature, the m-Nitrophenol (m-NPH) appears in two polymorphicstructures: orthorhombic and monoclinic forms. In the present work, we shall focus on themonoclinic form of this compound which has a centrosymmetric structure with the spacegroup P21/n. The molecular dipole moment has been estimated experimentally. Highresolution single crystal diffraction experiment was performed at low temperature withMoKα radiation. The crystal structure was refined using the multipolar model of Hansen andCoppens (1978). The molecular electron charge density distribution is described accurately.The study reveals the nature of inter-molecular interactions including charge transfer andhydrogen bonds. In this crystal, hydrogen bonds of moderate strength occur between thehydroxyl group and the O atom in the nitro one. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Genome-Wide Scan of the Gene Expression Kinetics of Salmonella enterica Serovar Typhi during Hyperosmotic Stress
Int. J. Mol. Sci. 2007, 8(2), 116-135; doi:10.3390/i8020116
Received: 10 December 2006 / Accepted: 12 February 2007 / Published: 16 February 2007
Cited by 18 | PDF Full-text (595 KB) | HTML Full-text | XML Full-text
Abstract
Salmonella enterica serovar Typhi is a human enteroinvasive pathogen that canovercome the stress caused by the high osmolarity of the human small intestine and causesystemic infection. To investigate the global transcriptional regulations of S. entericaserovar Typhi exposed to a hyperosmotic environment, a [...] Read more.
Salmonella enterica serovar Typhi is a human enteroinvasive pathogen that canovercome the stress caused by the high osmolarity of the human small intestine and causesystemic infection. To investigate the global transcriptional regulations of S. entericaserovar Typhi exposed to a hyperosmotic environment, a genomic oligo-DNA microarraycontaining 4474 Salmonella genes was prepared. A wild strain of S. enterica serovar TyphiGIFU10007 was grown in LB medium containing 50 mM NaCl to simulate a low osmoticenvironment. The hyperosmotic stress was simulated by an osmotic up-shift, whichincreased the concentration of NaCl in the LB from 50 mM to 300 mM. Genome-wide geneexpressions of S. enterica serovar Typhi at 15 min, 30 min, 60 min, and 120 min after theosmotic up-shift were investigated by the microarray analysis. Gene expression profiles insomewhat later stage (60 ~120 min) of the stress were quite different from those in the earlystage (0 ~ 30 min) of the stress. At 120 min after the osmotic stress, the expression levels of889 genes were obviously changed. However, expression levels of only 382 genes weresignificantly changed at 15 min after the osmotic stress. The expression levels of most SPI-1genes associated with invasion of the pathogen were increased at 120 min after the osmoticup-shift, but were not obviously changed at 15 min or 30 min after the osmotic stress.Expressions of a central regulatory gene, phoP, and sigma factor genes rpoE, rpoD, andrpoS were also changed with different profiles during the osmotic stress. These resultsindicated that the invasive ability of the pathogen is significantly increased after 2 h of hyperosmotic stress, and regulator PhoP and sigma factors RpoE, RpoD appear to participate in the network regulatory mechanisms that benefit the pathogen to adapt hyperosmotic environmental conditions. The later increased invasive ability of S. enterica serovar Typhi after hyperosmotic stress may be one reason why the pathogen performs invading in the distal ileum of human and not in areas of the upper small intestine. Full article
(This article belongs to the Special Issue Interaction of Biological Molecules)
Open AccessArticle Interactions between Cytochrome c and DNA Strands Self-Assembled at Gold Electrode
Int. J. Mol. Sci. 2007, 8(2), 136-144; doi:10.3390/i8020136
Received: 29 November 2006 / Accepted: 29 January 2007 / Published: 23 February 2007
Cited by 6 | PDF Full-text (153 KB) | HTML Full-text | XML Full-text
Abstract
In this work, we reported the investigation on the interaction between DNAstrands self-assembled at gold electrodes and an electron transfer protein, cytochrome c. Weobserved that cytochrome c exhibited well-defined electrochemistry in both double-strandedand single-stranded DNA films. This suggested that the electron transfer [...] Read more.
In this work, we reported the investigation on the interaction between DNAstrands self-assembled at gold electrodes and an electron transfer protein, cytochrome c. Weobserved that cytochrome c exhibited well-defined electrochemistry in both double-strandedand single-stranded DNA films. This suggested that the electron transfer reaction ofcytochrome c arose possibly due to the electron hopping along DNA strands rather thanwiring along the double helix. We also compared the heterogeneous electron transfer rate ofcytochrome c with that of a ruthenium complex, which further confirmed this mechanism. Full article
(This article belongs to the Special Issue Interaction of Biological Molecules)
Open AccessArticle A DFT-Based QSARs Study of Acetazolamide/Sulfanilamide Derivatives with Carbonic Anhydrase (CA-II) Isozyme Inhibitory Activity
Int. J. Mol. Sci. 2007, 8(2), 145-155; doi:10.3390/i8020145
Published: 23 February 2007
Cited by 15 | PDF Full-text (84 KB) | HTML Full-text | XML Full-text
Abstract
This study presents Quantitative Structure Activity Relationships (QSAR) studyon a pool of 18 bio-active sulfonamide compounds which includes five acetazolamidederivatives, eight sulfanilamide derivatives and five clinically used sulfonamides moleculesas drugs namely acetazolamide, methazolamide, dichlorophenamide, ethoxolamide anddorzolamide. For all the compounds, initial geometry [...] Read more.
This study presents Quantitative Structure Activity Relationships (QSAR) studyon a pool of 18 bio-active sulfonamide compounds which includes five acetazolamidederivatives, eight sulfanilamide derivatives and five clinically used sulfonamides moleculesas drugs namely acetazolamide, methazolamide, dichlorophenamide, ethoxolamide anddorzolamide. For all the compounds, initial geometry optimizations were carried out with amolecular mechanics (MM) method using the MM force fields. The lowest energyconformations of the compounds obtained by the MM method were further optimized by theDensity Functional Theory (DFT) method by employing Becke’s three-parameter hybridfunctional (B3LYP) and 6-31G (d) basis set. Molecular descriptors, dipole moment,electronegativity, total energy at 0 K, entropy at 298 K, HOMO and LUMO energiesobtained from DFT calculations provide valuable information and have a significant role inthe assessment of carbonic anhydrase (CA-II) inhibitory activity of the compounds. By usingthe multiple linear regression technique several QSAR models have been drown up with thehelp these calculated descriptors and carbonic anhydrase (CA-II) inhibitory data of themolecules. Among the obtained QSAR models presented in the study, statistically the mostsignificant one is a five parameters linear equation with the squared correlation coefficient R2 values of ca. 0.94 and the squared cross-validated correlation coefficient R2CV values of ca. 0.85. The results were discussed in the light of the main factors that influence theinhibitory activity of the carbonic anhydrase (CA-II) isozyme. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Cell Adhesion Regulates Expression of the Androgen Receptor and Coregulators in Different Prostate Cancer Cells
Int. J. Mol. Sci. 2007, 8(2), 156-165; doi:10.3390/i8020156
Received: 6 December 2006 / Accepted: 19 February 2007 / Published: 28 February 2007
PDF Full-text (341 KB) | HTML Full-text | XML Full-text
Abstract
Prostate cancer cells adhere to a tumor basement membrane, while secretoryepithelial cells reside in a suprabasal cell compartment. Since tumor cells are derived fromsuprabasal epithelial cells, they experience de-novo substratum adhesion in the context ofoncogenesis. We therefore analyzed whether cell-matrix adhesion could [...] Read more.
Prostate cancer cells adhere to a tumor basement membrane, while secretoryepithelial cells reside in a suprabasal cell compartment. Since tumor cells are derived fromsuprabasal epithelial cells, they experience de-novo substratum adhesion in the context ofoncogenesis. We therefore analyzed whether cell-matrix adhesion could affect the proteinexpression and activity of the AR. In this study, AR protein expression declined uponsuspension of BPH-1-AR cells, but not in PC-3-AR cells shown by Western blot. In a timecourse study, BPH-1 cell lost AR expression within 6 hours, and the synthetic androgen,R1881 reduced the loss of AR expression. We further explored the mechanism of AR loss insuspended BPH-1 cells. BPH-1-AR cells underwent apoptosis (anoikis) when suspended for2 - 5 hours. Suspension did not induce significant apoptosis or decreasing of AR expressionin PC-3 cells. Inhibition of apoptosis in suspended BPH-1-AR cells, either by expression ofBcl-2 or Bcl-xl or by treatment with Z-VAD, a caspase inhibitor, prevented loss of ARprotein. In contrast, the calpain protease inhibitor , ALLN, accelerated the loss of AR proteinexpression. Additionally, cell-matrix adhesion changed the expression of coregulators of ARin the mRNA level of prostate cancer cells. Our results demonstrate that AR proteinexpression was reduced through activation of cell death pathways, and thus indirectly through cell suspension in BPH-AR cells. The activity of AR can also be regulated by adhesion in PC-3-AR and LNCaP cells through affecting the coregulators level. Full article
Open AccessArticle An In Silico Method for Screening Nicotine Derivatives as Cytochrome P450 2A6 Selective Inhibitors Based on Kernel Partial Least Squares
Int. J. Mol. Sci. 2007, 8(2), 166-179; doi:10.3390/i8020166
Received: 13 December 2006 / Accepted: 19 January 2007 / Published: 28 February 2007
Cited by 21 | PDF Full-text (132 KB) | HTML Full-text | XML Full-text
Abstract
Nicotine and a variety of other drugs and toxins are metabolized by cytochromeP450 (CYP) 2A6. The aim of the present study was to build a quantitative structure-activityrelationship (QSAR) model to predict the activities of nicotine analogues on CYP2A6.Kernel partial least squares (K-PLS) [...] Read more.
Nicotine and a variety of other drugs and toxins are metabolized by cytochromeP450 (CYP) 2A6. The aim of the present study was to build a quantitative structure-activityrelationship (QSAR) model to predict the activities of nicotine analogues on CYP2A6.Kernel partial least squares (K-PLS) regression was employed with the electro-topologicaldescriptors to build the computational models. Both the internal and external predictabilitiesof the models were evaluated with test sets to ensure their validity and reliability. As acomparison to K-PLS, a standard PLS algorithm was also applied on the same training andtest sets. Our results show that the K-PLS produced reasonable results that outperformed thePLS model on the datasets. The obtained K-PLS model will be helpful for the design ofnovel nicotine-like selective CYP2A6 inhibitors. Full article
(This article belongs to the Special Issue Interaction of Biological Molecules)

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