Research

395 KiB

Open AccessArticle

The Molecular Structure and Vibrational Spectrum of 6-bromo-8-thia-1,4-epoxybicyclo[4.3.0]non-2-ene

by Hakan Arslan and Aydın Demircan

Int. J. Mol. Sci. 2007, 8(11), 1064-1082; https://doi.org/10.3390/i8111064 - 29 Oct 2007

Cited by 9 | Viewed by 17487

Geometric parameters and FT-IR spectrum of 6-bromo-8-thia-1,4-epoxybicyclo[4.3.0]non-2-ene were computed by the HF, B3LYP, B3PW91 andmPW1PW91 methods in conjunction with the 6-31G(d,p) basis set. The calculated IRspectra are in a good agreement with the observed FT-IR spectrum. A general betterperformance of B3LYP, B3PW91 and [...] Read more.

Geometric parameters and FT-IR spectrum of 6-bromo-8-thia-1,4-epoxybicyclo[4.3.0]non-2-ene were computed by the HF, B3LYP, B3PW91 andmPW1PW91 methods in conjunction with the 6-31G(d,p) basis set. The calculated IRspectra are in a good agreement with the observed FT-IR spectrum. A general betterperformance of B3LYP, B3PW91 and mPW1PW91 versus HF was quantitativelycharacterized by using PAVF 1.0 program. Optimal uniform scaling factors calculated forthe title compound are 0.8952, 0.9552, 0.9520 and 0.9456 for HF, B3LYP, B3PW91 andMPW1PW91 methods, respectively. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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346 KiB

Open AccessArticle

A Fragment-Based Scoring Function to Re-rank ATP Docking Results

by Timothy V. Pyrkov and Roman G. Efremov

Int. J. Mol. Sci. 2007, 8(11), 1083-1094; https://doi.org/10.3390/i8111083 - 31 Oct 2007

Cited by 9 | Viewed by 12332

Abstract

ATP is involved in numerous biochemical reactions in living cells interacting withdifferent proteins. Molecular docking simulations provide considerable insight into theproblem of molecular recognition of this substrate. To improve the selection of correctATP poses among those generated by docking algorithms we propose a [...] Read more.

ATP is involved in numerous biochemical reactions in living cells interacting withdifferent proteins. Molecular docking simulations provide considerable insight into theproblem of molecular recognition of this substrate. To improve the selection of correctATP poses among those generated by docking algorithms we propose a post-docking rerankingcriterion. The method is based on detailed analysis of the intermolecularinteractions in 50 high-resolution 3D-structures of ATP-protein complexes. A distinctivenew feature of the proposed method is that the ligand molecule is divided into fragmentsthat differ in their physical properties. The placement of each of them into the bindingsite is judged separately by different criteria, thus avoiding undesirable averaging of thescoring function terms by highlighting those relevant for particular fragments. Thescoring performance of the new criteria was tested with the docking solutions for ATPproteincomplexes and a significant improvement in the selection of correct dockingposes was observed, as compared to the standard scoring function. Full article

(This article belongs to the Section Molecular Recognition)

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475 KiB

Open AccessArticle

Antiproliferation of Hepatoma Cell and Progression of Cell Cycle as Affected by Isoflavone Extracts from Soybean Cake

by Tsai-Hua Kao, Rwei-Fen S. Huang and Bing-Huei Chen

Int. J. Mol. Sci. 2007, 8(11), 1095-1110; https://doi.org/10.3390/i8111092 - 01 Nov 2007

Cited by 11 | Viewed by 8978

Abstract

The objectives of this study were to isolate various isoflavone fractions andextracts from soybean cake by preparative column chromatography and compare themwith isoflavone standards with regards to inhibition of HepG2 cancer cell proliferation.Four fractions, including malonylglucoside, glucoside, acetylglucoside and aglycone, andtwo isoflavone extracts, [...] Read more.

The objectives of this study were to isolate various isoflavone fractions andextracts from soybean cake by preparative column chromatography and compare themwith isoflavone standards with regards to inhibition of HepG2 cancer cell proliferation.Four fractions, including malonylglucoside, glucoside, acetylglucoside and aglycone, andtwo isoflavone extracts, ISO-1 and ISO-2, were collected for evaluation. MTT test resultsshowed that most treatments were slightly protective against HepG2 cell growth at a lowdose of isoflavone (5 and 10 μg/mL). However, at elevated concentration of isoflavone(20-50 μg/mL), both aglycone and acetylglucoside fractions as well as a mixture ofisoflavone standards were the most effective in inhibition, demonstrating a possiblesynergistic phenomenon. Genistein showed a better retardation effect than daidzein. Forcell cycle analysis, both aglycone and acetylglucoside fractions and a mixture ofisoflavone standards exhibited a high G2/M ratio, correlating well with the result of MTTtest. The presence of some other functional components in soybean cake like saponinsand phenolic compounds may also play a vital role in inhibiting HepG2 cell growth. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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312 KiB

Open AccessArticle

Analysis of Phenacylester Derivatives of Fatty Acids from Human Skin Surface Sebum by Reversed-Phase HPLC: Chromatographic Mobility as a Function of Physico-Chemical Properties

by Juliana Bodoprost and Helmut Rosemeyer

Int. J. Mol. Sci. 2007, 8(11), 1111-1124; https://doi.org/10.3390/i8111111 - 21 Nov 2007

Cited by 38 | Viewed by 10964

Abstract

A set of 13 fatty acids was transformed into their phenacyl esters by reaction withphenacyl bromide in acetonitrile using 18-crown-6 as phase-transfer catalyst. Conditions forthe RP-18 HPL chromatographic separation of most of the esters has been worked out.Using this standard the fatty acid [...] Read more.

A set of 13 fatty acids was transformed into their phenacyl esters by reaction withphenacyl bromide in acetonitrile using 18-crown-6 as phase-transfer catalyst. Conditions forthe RP-18 HPL chromatographic separation of most of the esters has been worked out.Using this standard the fatty acid spectra from skin surface sebum lipids of 17 test personswas taken after microwave-assisted hydrolysis, neutralization and extraction with n-hexane.Quantitative evaluation of the chromatograms exhibits that oleic acid predominates in thesebum of all test persons. In the second part of the work the chromatographic mobility (REvalues) of fatty acid phenacyl esters is correlated with calculated physico-chemicalparameters of the corresponding acids. The best linear correlation was found between the REand the logP values. This is helpful for the structural elucidation of un-identified fatty acidsin a chromatogram. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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372 KiB

Open AccessArticle

Chromatographic Retention Times of Polychlorinated Biphenyls: from Structural Information to Property Characterization

by Lorentz Jäntschi, Sorana D. Bolboaca and Mircea V. Diudea

Int. J. Mol. Sci. 2007, 8(11), 1125-1157; https://doi.org/10.3390/i8111125 - 22 Nov 2007

Cited by 20 | Viewed by 9222

Abstract

The paper presents a unitary approach of the use of a Molecular DescriptorsFamily in structure-property/activity relationships, particularly in modelling thechromatographic retention times of polychlorinated biphenyls. Starting from molecularstructure, viewed as a graph, and considering the bonds and bond types, atom types andoften the [...] Read more.

The paper presents a unitary approach of the use of a Molecular DescriptorsFamily in structure-property/activity relationships, particularly in modelling thechromatographic retention times of polychlorinated biphenyls. Starting from molecularstructure, viewed as a graph, and considering the bonds and bond types, atom types andoften the 3D geometry of the molecule, a huge family of molecular descriptors called MDFwas calculated. A preliminary selection of MDF members was done by simple linearregression (LR) against the measured property. The best fitted MDF subset is thensubmitted to multivariate linear regression (MLR) analysis in order to find the best pairs ofMDF members that produce a reliable QSPR (Quantitative Structure-PropertyRelationship) model. The predictive capability was finally tested by randomly splitting ofdata into training and test sets. The best obtained models are presented and the results arediscussed. Full article

(This article belongs to the Special Issue The Chemical Bond and Bonding)

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177 KiB

Open AccessArticle

Electron-Capture Cross Sections of Ground-State O₂⁺ Recoil Ions in Slow Collisions with H₂ and O₂

by Asad T. Hasan and Tom J. Gray

Int. J. Mol. Sci. 2007, 8(11), 1158-1164; https://doi.org/10.3390/i8111158 - 22 Nov 2007

Cited by 2 | Viewed by 7050

Abstract

We report the measured total charge-transfer (electron-capture) cross sectionsfor the ground state O₂⁺ (X²πg) ions with H₂ and O₂ molecular gases in the collisionenergy range between 0.50 and 2 keV. The time-of-flight technique has been used tomeasure [...] Read more.

We report the measured total charge-transfer (electron-capture) cross sectionsfor the ground state O₂⁺ (X²πg) ions with H₂ and O₂ molecular gases in the collisionenergy range between 0.50 and 2 keV. The time-of-flight technique has been used tomeasure the fast neutral products from O₂⁺ charge transfer reactions. The analyzedprocess has cross sections that continue to increase slowly, as a function of incidentenergy. Measured cross sections for O₂⁺ H₂, O₂ systems are compared with previouslyavailable experimental and theoretical results in the literature. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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535 KiB

Open AccessArticle

Inhibition of Acetylcholinesterase in Different Structures of the Rat Brain Following Soman Intoxication Pretreated with Huperzine A

by Jiri Bajgar, Petr Hajek, Jana Karasova, Dasa Slizova, Otakar Krs, Kamil Kuca, Daniel Jun, Josef Fusek and Lukas Capek

Int. J. Mol. Sci. 2007, 8(11), 1165-1176; https://doi.org/10.3390/i8111165 - 26 Nov 2007

Cited by 18 | Viewed by 9363

Abstract

Acetylcholinesterase (AChE) activities in different brain parts were determinedquantitatively in rats treated with huperzine A, soman, and huperzine A followed bysoman, using histochemical and biochemical methods. Following soman intoxication (1.2x LD50, i.m.), AChE activity was decreased to 30-80% of control values depending on [...] Read more.

Acetylcholinesterase (AChE) activities in different brain parts were determinedquantitatively in rats treated with huperzine A, soman, and huperzine A followed bysoman, using histochemical and biochemical methods. Following soman intoxication (1.2x LD50, i.m.), AChE activity was decreased to 30-80% of control values depending on thebrain structure. The most sensitive area was the frontal cortex and the most relativelyresistant was ncl. ruber. Huperzine A treatment only caused a change in AChE activityvarying from 70 to 100 % of control values. In rats pretreated with huperzine A andintoxicated with soman, AChE activity was significantly higher than that observed aftersoman. In these animals, survival of rats pretreated with huperzine was observed whilethe mortality of unpretreated animals was near to 80 %. The results suggest that huperzineA is good candidate for further study for clinical use as a prophylactic drug against nerveagent poisoning. Full article

(This article belongs to the Section Biochemistry)

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288 KiB

Open AccessArticle

The Signaling Cascades of Ginkgolide B-Induced Apoptosis in MCF-7 Breast Cancer Cells

by Wen-Hsiung Chan

Int. J. Mol. Sci. 2007, 8(11), 1177-1195; https://doi.org/10.3390/i8111177 - 27 Nov 2007

Cited by 8 | Viewed by 8548

Abstract

Ginkgolide B, the major active component of Ginkgo biloba extracts, can bothstimulate and inhibit apoptotic signaling. Here, we demonstrate that ginkgolide B caninduce the production of reactive oxygen species in MCF-7 breast cancer cells, leading toan increase in the intracellular concentrations of cytoplasmic [...] Read more.

Ginkgolide B, the major active component of Ginkgo biloba extracts, can bothstimulate and inhibit apoptotic signaling. Here, we demonstrate that ginkgolide B caninduce the production of reactive oxygen species in MCF-7 breast cancer cells, leading toan increase in the intracellular concentrations of cytoplasmic free Ca²⁺ and nitric oxide(NO), loss of mitochondrial membrane potential (MMP), activation of caspase-9 and -3,and increase the mRNA expression levels of p53 and p21, which are known to be involvedin apoptotic signaling. In addition, prevention of ROS generation by pretreatment withN-acetyl cysteine (NAC) could effectively block intracellular Ca²⁺ concentrationsincreases and apoptosis in ginkgolide B-treated MCF-7 cells. Moreover, pretreatment withnitric oxide (NO) scavengers could inhibit ginkgolide B-induced MMP change andsequent apoptotic processes. Overall, our results signify that both ROS and NO playedimportant roles in ginkgolide B-induced apoptosis of MCF-7 cells. Based on these studyresults, we propose a model for ginkgolide B-induced cell apoptosis signaling cascades inMCF-7 cells. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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Int. J. Mol. Sci., Volume 8, Issue 11 (November 2007) – 8 articles , Pages 1064-1195

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