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Int. J. Mol. Sci., Volume 12, Issue 8 (August 2011) – 48 articles , Pages 4758-5460

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Open AccessArticle
Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes
Int. J. Mol. Sci. 2011, 12(8), 5449-5460; https://doi.org/10.3390/ijms12085449 - 24 Aug 2011
Cited by 21 | Viewed by 4313
Abstract
Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa [...] Read more.
Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm. Full article
(This article belongs to the Section Biochemistry)
Open AccessArticle
Antioxidant, Antimicrobial and Antiproliferative Activities of Five Lichen Species
Int. J. Mol. Sci. 2011, 12(8), 5428-5448; https://doi.org/10.3390/ijms12085428 - 23 Aug 2011
Cited by 102 | Viewed by 7142
Abstract
The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of gallic [...] Read more.
The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of gallic acid equivalent (GA)/g of extract and the total flavonoid content from 20.14 to 44.43 mg of rutin equivalent (Ru)/g of extract. The antioxidant capacities of the lichen extracts were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals scavenging. Hypogymnia physodes with the highest phenolic content showed the strongest DPPH radical scavenging effect. Further, the antimicrobial potential of the lichen extracts was determined by a microdilution method on 29 microorganisms, including 15 strains of bacteria, 10 species of filamentous fungi and 4 yeast species. A high antimicrobial activity of all the tested extracts was observed with more potent inhibitory effects on the growth of Gram (+) bacteria. The highest antimicrobial activity among lichens was demonstrated by Hypogymnia physodes and Cladonia foliacea. Finally, the antiproliferative activity of the lichen extracts was explored on the colon cancer adenocarcinoma cell line HCT-116 by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) viability assay and acridine orange/ethidium bromide staining. The methanol extracts of Hypogymnia physodes and Cladonia foliacea showed a better cytotoxic activity than the other extracts. All lichen species showed the ability to induce apoptosis of HCT-116 cells. Full article
(This article belongs to the Section Biochemistry)
Open AccessCommunication
Preparation and Microcosmic Structural Analysis of Recording Coating on Inkjet Printing Media
Int. J. Mol. Sci. 2011, 12(8), 5422-5427; https://doi.org/10.3390/ijms12085422 - 23 Aug 2011
Cited by 2 | Viewed by 4278
Abstract
Preparation of recording coating on inkjet printing (RC-IJP) media was proposed. The microstructure and roughness of RC-IJP was analyzed by scanning electron microscopy (SEM) and atomic force microscope (AFM). The surface infiltration process of RC-IJP was studied by a liquid infiltration instrument. The [...] Read more.
Preparation of recording coating on inkjet printing (RC-IJP) media was proposed. The microstructure and roughness of RC-IJP was analyzed by scanning electron microscopy (SEM) and atomic force microscope (AFM). The surface infiltration process of RC-IJP was studied by a liquid infiltration instrument. The distribution of C, O and Si composites on recording coating surface is analyzed by energy dispersive spectrum (EDS). The transmission electron microscopy (TEM) analysis showed that the nanoscale silica could be dissolved uniformly in water. Finally, the print color is shown clearly by the preparative recording coating. Full article
(This article belongs to the Section Materials Science)
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Open AccessReview
Self-Assembly in the Ferritin Nano-Cage Protein Superfamily
Int. J. Mol. Sci. 2011, 12(8), 5406-5421; https://doi.org/10.3390/ijms12085406 - 22 Aug 2011
Cited by 70 | Viewed by 6280
Abstract
Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, [...] Read more.
Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2011)
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Open AccessArticle
The hsp 16 Gene of the Probiotic Lactobacillus acidophilus Is Differently Regulated by Salt, High Temperature and Acidic Stresses, as Revealed by Reverse Transcription Quantitative PCR (qRT-PCR) Analysis
Int. J. Mol. Sci. 2011, 12(8), 5390-5405; https://doi.org/10.3390/ijms12085390 - 22 Aug 2011
Cited by 14 | Viewed by 4884
Abstract
Small heat shock proteins (sHsps) are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR) procedure was developed and used to quantify the transcript level of a small heat shock gene [...] Read more.
Small heat shock proteins (sHsps) are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR) procedure was developed and used to quantify the transcript level of a small heat shock gene (shs) in the probiotic bacterium Lactobacillus acidophilus NCFM, under stress conditions such as heat (45 °C and 53 °C), bile (0.3% w/v), hyperosmosis (1 M and 2.5 M NaCl), and low pH value (pH 4). The shs gene of L. acidophilus NCFM was induced by salt, high temperature and acidic stress, while repression was observed upon bile stress. Analysis of the 5' noncoding region of the hsp16 gene reveals the presence of an inverted repeat (IR) sequence (TTAGCACTC-N9-GAGTGCTAA) homologue to the controlling IR of chaperone expression (CIRCE) elements found in the upstream regulatory region of Gram-positive heat shock operons, suggesting that the hsp16 gene of L. acidophilus might be transcriptionally controlled by HrcA. In addition, the alignment of several small heat shock proteins identified so far in lactic acid bacteria, reveals that the Hsp16 of L. acidophilus exhibits a strong evolutionary relationship with members of the Lactobacillus acidophilus group. Full article
(This article belongs to the Section Biochemistry)
Open AccessReview
p66Shc Aging Protein in Control of Fibroblasts Cell Fate
Int. J. Mol. Sci. 2011, 12(8), 5373-5389; https://doi.org/10.3390/ijms12085373 - 22 Aug 2011
Cited by 13 | Viewed by 4960
Abstract
Reactive oxygen species (ROS) are wieldy accepted as one of the main factors of the aging process. These highly reactive compounds modify nucleic acids, proteins and lipids and affect the functionality of mitochondria in the first case and ultimately of the cell. Any [...] Read more.
Reactive oxygen species (ROS) are wieldy accepted as one of the main factors of the aging process. These highly reactive compounds modify nucleic acids, proteins and lipids and affect the functionality of mitochondria in the first case and ultimately of the cell. Any agent or genetic modification that affects ROS production and detoxification can be expected to influence longevity. On the other hand, genetic manipulations leading to increased longevity can be expected to involve cellular changes that affect ROS metabolism. The 66-kDa isoform of the growth factor adaptor Shc (p66Shc) has been recognized as a relevant factor to the oxygen radical theory of aging. The most recent data indicate that p66Shc protein regulates life span in mammals and its phosphorylation on serine 36 is important for the initiation of cell death upon oxidative stress. Moreover, there is strong evidence that apart from aging, p66Shc may be implicated in many oxidative stress-associated pathologies, such as diabetes, mitochondrial and neurodegenerative disorders and tumorigenesis. This article summarizes recent knowledge about the role of p66Shc in aging and senescence and how this protein can influence ROS production and detoxification, focusing on studies performed on skin and skin fibroblasts. Full article
(This article belongs to the Special Issue Oxidative Stress and Mitochondria)
Open AccessReview
Structure and Dynamics of Reentrant Nematics: Any Open Questions after Almost 40 Years?
Int. J. Mol. Sci. 2011, 12(8), 5352-5372; https://doi.org/10.3390/ijms12085352 - 22 Aug 2011
Cited by 11 | Viewed by 4743
Abstract
Liquid crystals have attracted enormous interest because of the variety of their phases and richness of their application. The interplay of general physical symmetries and specific molecular features generates a myriad of different phenomena. A surprising behavior of liquid crystals is the reentrancy [...] Read more.
Liquid crystals have attracted enormous interest because of the variety of their phases and richness of their application. The interplay of general physical symmetries and specific molecular features generates a myriad of different phenomena. A surprising behavior of liquid crystals is the reentrancy of phases as temperature, pressure, or concentration are varied. Here, we review the main experimental facts and the different theoretical scenarios that have guided the understanding of bulk reentrant nematics. Recently, some computer simulations of a system confined to nanoscopic scales have found new dynamical features of the reentrant nematic phase. We discuss this prediction in relation with the available experimental evidence on reentrant nematics and with the dynamics of liquids in strongly confined environments. Full article
(This article belongs to the Special Issue Liquid Crystals 2011)
Open AccessCommunication
Spin Transition Sensors Based on β-Amino-Acid 1,2,4-Triazole Derivative
Int. J. Mol. Sci. 2011, 12(8), 5339-5351; https://doi.org/10.3390/ijms12085339 - 18 Aug 2011
Cited by 19 | Viewed by 5121
Abstract
A β-aminoacid ester was successfully derivatized to yield to 4H-1,2-4-triazol-4-yl-propionate (βAlatrz) which served as a neutral bidentate ligand in the 1D coordination polymer [Fe(βAlatrz)3](CF3SO3)2·0.5H2O (1·0.5H [...] Read more.
A β-aminoacid ester was successfully derivatized to yield to 4H-1,2-4-triazol-4-yl-propionate (βAlatrz) which served as a neutral bidentate ligand in the 1D coordination polymer [Fe(βAlatrz)3](CF3SO3)2·0.5H2O (1·0.5H2O). The temperature dependence of the high-spin molar fraction derived from 57Fe Mossbauer spectroscopy recorded on cooling below room temperature reveals an exceptionally abrupt single step transition between high-spin and low-spin states with a hysteresis loop of width 4 K (Tc = 232 K and Tc = 228 K) in agreement with magnetic susceptibility measurements. The material presents striking reversible thermochromism from white, at room temperature, to pink on quench cooling to liquid nitrogen, and acts as an alert towards temperature variations. The phase transition is of first order, as determined by differential scanning calorimetry, with transition temperatures matching the ones determined by SQUID and Mössbauer spectroscopy. The freshly prepared sample of 1·0.5H2O, dried in air, was subjected to annealing at 390 K, and the obtained white compound [Fe(βAlatrz)3](CF3SO3)2 (1) was found to exhibit a similar spin transition curve however much temperature was increased by (Tc = 252 K and Tc = 248 K). The removal of lattice water molecules from 1·0.5H2O is not accompanied by a change of the morphology and of the space group, and the chain character is preserved. However, an internal pressure effect stabilizing the low-spin state is evidenced. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Electronics)
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Open AccessArticle
Effect of Filler Size and Temperature on Packing Stress and Viscosity of Resin-composites
Int. J. Mol. Sci. 2011, 12(8), 5330-5338; https://doi.org/10.3390/ijms12085330 - 18 Aug 2011
Cited by 8 | Viewed by 3714
Abstract
The objective of this study was to investigate the effect of filler size on the packing stress and viscosity of uncured resin-composite at 23 °C and 37 °C. A precision instrument used was designed upon the penetrometer principle. Eight resin-composite materials were tested. [...] Read more.
The objective of this study was to investigate the effect of filler size on the packing stress and viscosity of uncured resin-composite at 23 °C and 37 °C. A precision instrument used was designed upon the penetrometer principle. Eight resin-composite materials were tested. Packing-stress ranged from 2.60 to 0.43 MPa and viscosity ranged from 2.88 to 0.02 MPa.s at 23 °C. Values for both properties were reduced significantly at 37 °C. Statistical analysis, by ANOVA and post hoc methods, were carried out to check any significant differences between materials tested (P < 0.05). Conclusions: Filler size and distribution will affect the viscosity and packing of resin-composites during cavity placement. Full article
(This article belongs to the Special Issue Dental Materials)
Open AccessArticle
Microwave-Assisted Extraction of Oleanolic Acid and Ursolic Acid from Ligustrum lucidum Ait
Int. J. Mol. Sci. 2011, 12(8), 5319-5329; https://doi.org/10.3390/ijms12085319 - 18 Aug 2011
Cited by 45 | Viewed by 7055
Abstract
Oleanolic acid and ursolic acid are the main active components in fruit of Ligustrum lucidum Ait, and possess anticancer, antimutagenic, anti-inflammatory, antioxidative and antiprotozoal activities. In this study, microwave-assisted extraction of oleanolic acid and ursolic acid from Ligustrum lucidum was investigated with HPLC-photodiode [...] Read more.
Oleanolic acid and ursolic acid are the main active components in fruit of Ligustrum lucidum Ait, and possess anticancer, antimutagenic, anti-inflammatory, antioxidative and antiprotozoal activities. In this study, microwave-assisted extraction of oleanolic acid and ursolic acid from Ligustrum lucidum was investigated with HPLC-photodiode array detection. Effects of several experimental parameters, such as type and concentration of extraction solvent, ratio of liquid to material, microwave power, extraction temperature and microwave time, on the extraction efficiencies of oleanolic acid and ursolic acid from Ligustrum lucidum were evaluated. The influence of experimental parameters on the extraction efficiency of ursolic acid was more significant than that of oleanolic acid (p < 0.05). The optimal extraction conditions were 80% ethanol aqueous solution, the ratio of material to liquid was 1:15, and extraction for 30 min at 70 °C under microwave irradiation of 500 W. Under optimal conditions, the yields of oleanolic acid and ursolic acid were 4.4 ± 0.20 mg/g and 5.8 ± 0.15 mg/g, respectively. The results obtained are helpful for the full utilization of Ligustrum lucidum, which also indicated that microwave-assisted extraction is a very useful method for extraction of oleanolic acid and ursolic acid from plant materials. Full article
(This article belongs to the Section Biochemistry)
Open AccessReview
Reviewing Ligand-Based Rational Drug Design: The Search for an ATP Synthase Inhibitor
Int. J. Mol. Sci. 2011, 12(8), 5304-5318; https://doi.org/10.3390/ijms12085304 - 17 Aug 2011
Cited by 30 | Viewed by 6010
Abstract
Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design process. [...] Read more.
Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design process. In this paper, by describing the search for an ATP synthase inhibitor, we review two frequently used approaches in ligand-based drug design: The pharmacophore model and the quantitative structure-activity relationship (QSAR) method. Moreover, since ATP synthase ligands are potentially useful drugs in cancer therapy, pharmacophore models were constructed to pave the way for novel inhibitor designs. Full article
(This article belongs to the Special Issue A Systematic Development Method for Rational Drug Design)
Open AccessArticle
Characterization of Thermophilic Halotolerant Aeribacillus pallidus TD1 from Tao Dam Hot Spring, Thailand
Int. J. Mol. Sci. 2011, 12(8), 5294-5303; https://doi.org/10.3390/ijms12085294 - 17 Aug 2011
Cited by 24 | Viewed by 4615
Abstract
The bacterial strain TD1 was isolated from Tao Dam hot spring in Thailand. Strain TD1 was Gram positive, rod-shaped, aerobic, motile, and endospore forming. The cell was 2.0–40 mm in length and about 0.4 mm in diameter. The optimum growth occurred at 55–60 [...] Read more.
The bacterial strain TD1 was isolated from Tao Dam hot spring in Thailand. Strain TD1 was Gram positive, rod-shaped, aerobic, motile, and endospore forming. The cell was 2.0–40 mm in length and about 0.4 mm in diameter. The optimum growth occurred at 55–60 °C and at pH 7–8. Strain TD1 was able to grow on medium containing up to 10% NaCl. The DNA G+C content was 38.9 mol%. The cellular fatty acid content was mainly C16:0, which comprised 25.04% of the total amount of cellular fatty acid. 16S rDNA showed 99% identity to Aeribacillus pallidus DSM 3670T. Bayesian tree analysis strongly supported the idea that strain TD1 is affiliated with genus Aeribacillus, as Aeribacillus pallidus strain TD1. Although the 16S rDNA of A. pallidus strain TD1 is similar to that of A. pallidus DSM 3670T, some physiological properties and the cellular fatty acid profiles differ significantly. A. pallidus strain TD1 can produce extracellular pectate lyase, which has not been reported elsewhere for other bacterial strains in the genus Aeribacillus. A. pallidus strain TD1 may be a good candidate as a pectate lyase producer, which may have useful industrial applications. Full article
(This article belongs to the Section Biochemistry)
Open AccessReview
New Aspects of Mitochondrial Uncoupling Proteins (UCPs) and Their Roles in Tumorigenesis
Int. J. Mol. Sci. 2011, 12(8), 5285-5293; https://doi.org/10.3390/ijms12085285 - 17 Aug 2011
Cited by 48 | Viewed by 5122
Abstract
Uncoupling proteins (UCPs) belong to a family of mitochondrial carrier proteins that are present in the mitochondrial inner membrane. UCP1 was first identified followed by its two homologs, UCP2 and UCP3. The physiological functions of UCP include lowering mitochondrial membrane potential and dissipating [...] Read more.
Uncoupling proteins (UCPs) belong to a family of mitochondrial carrier proteins that are present in the mitochondrial inner membrane. UCP1 was first identified followed by its two homologs, UCP2 and UCP3. The physiological functions of UCP include lowering mitochondrial membrane potential and dissipating metabolic energy as heat. However, UCP can be dysregulated and may contribute to the pathogenesis of metabolic disorders and obesity. Recent studies suggest that UCP also plays a role in neurodegenerative diseases and atherosclerosis. In addition, the widely expressed UCP, UCP2, has been shown to be upregulated in a number of aggressive human cancers. One mechanism of UCP2 upregulation in these cancers is due to oxidative stress, and elevated UCP2 in turn reduces oxidative stress, which provides a growth advantage for these cancers. Nevertheless, new studies suggest UCP2 may interact with oncogenes and tumor suppressor genes, providing a potential new mechanism of how UCP2 contributes to cancer development. In this review, the evidence supporting the role of UCPs in diseases other than diabetes and obesity, the reports on how UCP is regulated in cancer cells, and how UCP may regulate p53 will be discussed. Full article
(This article belongs to the Section Biochemistry)
Open AccessReview
FK506-Binding Protein 22 from a Psychrophilic Bacterium, a Cold Shock-Inducible Peptidyl Prolyl Isomerase with the Ability to Assist in Protein Folding
Int. J. Mol. Sci. 2011, 12(8), 5261-5284; https://doi.org/10.3390/ijms12085261 - 17 Aug 2011
Cited by 22 | Viewed by 4978
Abstract
Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at [...] Read more.
Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at low temperatures is much slower than that at higher temperatures and may cause problems in protein folding. However, the mechanisms by which PPIases are involved in cold adaptation remain unclear. Here we used FK506-binding protein 22, a cold shock protein from the psychrophilic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) as a model protein to decipher the involvement of PPIases in cold adaptation. SIB1 FKBP22 is homodimer that assumes a V-shaped structure based on a tertiary model. Each monomer consists of an N-domain responsible for dimerization and a C-catalytic domain. SIB1 FKBP22 is a typical cold-adapted enzyme as indicated by the increase of catalytic efficiency at low temperatures, the downward shift in optimal temperature of activity and the reduction in the conformational stability. SIB1 FKBP22 is considered as foldase and chaperone based on its ability to catalyze refolding of a cis-proline containing protein and bind to a folding intermediate protein, respectively. The foldase and chaperone activites of SIB1 FKBP22 are thought to be important for cold adaptation of Shewanella sp. SIB1. These activities are also employed by other PPIases for being involved in cold adaptation of various microorganisms. Despite other biological roles of PPIases, we proposed that foldase and chaperone activities of PPIases are the main requirement for overcoming the cold-stress problem in microorganisms due to folding of proteins. Full article
(This article belongs to the Special Issue Protein Folding 2011)
Open AccessCommunication
Sinanodonta woodiana (Mollusca: Bivalvia: Unionidae): Isolation and Characterization of the First Microsatellite Markers
Int. J. Mol. Sci. 2011, 12(8), 5255-5260; https://doi.org/10.3390/ijms12085255 - 17 Aug 2011
Cited by 7 | Viewed by 4326
Abstract
Sinanodonta woodiana (Lea, 1834) is a large Unionid species with a real invasion success. It colonized Europe, Central America, the Indonesian Islands and recently North America. The species life cycle involves a larval parasitic stage on freshwater fish species which contributes to the [...] Read more.
Sinanodonta woodiana (Lea, 1834) is a large Unionid species with a real invasion success. It colonized Europe, Central America, the Indonesian Islands and recently North America. The species life cycle involves a larval parasitic stage on freshwater fish species which contributes to the spread of the mussel. In this paper we describe, for the first time, eight polymorphic microsatellite loci for the species Sinanodonta woodiana. The genetic screening of individuals confirmed that all loci were highly polymorphic. The number of alleles per locus ranged from 7 to 14 and the observed heterozygosity ranged from 0.650 to 0.950. These loci should prove useful to study the species population genetics which could help to infer important aspects of the invasion process. Full article
(This article belongs to the Section Biochemistry)
Open AccessArticle
Effects of Nitrogen Fertilization on Synthesis of Primary and Secondary Metabolites in Three Varieties of Kacip Fatimah (Labisia Pumila Blume)
Int. J. Mol. Sci. 2011, 12(8), 5238-5254; https://doi.org/10.3390/ijms12085238 - 16 Aug 2011
Cited by 69 | Viewed by 4747
Abstract
A split plot 3 by 4 experiment was designed to examine the impact of 15-week variable levels of nitrogen fertilization (0, 90, 180 and 270 kg N/ha) on the characteristics of total flavonoids (TF), total phenolics (TP), total non structurable carbohydrate (TNC), net [...] Read more.
A split plot 3 by 4 experiment was designed to examine the impact of 15-week variable levels of nitrogen fertilization (0, 90, 180 and 270 kg N/ha) on the characteristics of total flavonoids (TF), total phenolics (TP), total non structurable carbohydrate (TNC), net assimilation rate, leaf chlorophyll content, carbon to nitrogen ratio (C/N), phenyl alanine lyase activity (PAL) and protein content, and their relationships, in three varieties of Labisia pumila Blume (alata, pumila and lanceolata). The treatment effects were solely contributed by nitrogen application; there was neither varietal nor interaction effect observed. As nitrogen levels increased from 0 to 270 kg N/ha, the production of TNC was found to decrease steadily. Production of TF and TP reached their peaks under 0 followed by 90, 180 and 270 kg N/ha treatment. However, net assimilation rate was enhanced as nitrogen fertilization increased from 0 to 270 kg N/ha. The increase in production of TP and TF under low nitrogen levels (0 and 90 kg N/ha) was found to be correlated with enhanced PAL activity. The enhancement in PAL activity was followed by reduction in production of soluble protein under low nitrogen fertilization indicating more availability of amino acid phenyl alanine (phe) under low nitrogen content that stimulate the production of carbon based secondary metabolites (CBSM). The latter was manifested by high C/N ratio in L. pumila plants. Full article
(This article belongs to the Section Biochemistry)
Open AccessReview
Mechanisms of Mycotoxin-Induced Neurotoxicity through Oxidative Stress-Associated Pathways
Int. J. Mol. Sci. 2011, 12(8), 5213-5237; https://doi.org/10.3390/ijms12085213 - 15 Aug 2011
Cited by 79 | Viewed by 6645
Abstract
Among many mycotoxins, T-2 toxin, macrocyclic trichothecenes, fumonisin B1 (FB1) and ochratochin A (OTA) are known to have the potential to induce neurotoxicity in rodent models. T-2 toxin induces neuronal cell apoptosis in the fetal and adult brain. Macrocyclic trichothecenes [...] Read more.
Among many mycotoxins, T-2 toxin, macrocyclic trichothecenes, fumonisin B1 (FB1) and ochratochin A (OTA) are known to have the potential to induce neurotoxicity in rodent models. T-2 toxin induces neuronal cell apoptosis in the fetal and adult brain. Macrocyclic trichothecenes bring about neuronal cell apoptosis and inflammation in the olfactory epithelium and olfactory bulb. FB1 induces neuronal degeneration in the cerebral cortex, concurrent with disruption of de novo ceramide synthesis. OTA causes acute depletion of striatal dopamine and its metabolites, accompanying evidence of neuronal cell apoptosis in the substantia nigra, striatum and hippocampus. This paper reviews the mechanisms of neurotoxicity induced by these mycotoxins especially from the viewpoint of oxidative stress-associated pathways. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle
A Comparative Reverse Docking Strategy to Identify Potential Antineoplastic Targets of Tea Functional Components and Binding Mode
Int. J. Mol. Sci. 2011, 12(8), 5200-5212; https://doi.org/10.3390/ijms12085200 - 15 Aug 2011
Cited by 26 | Viewed by 4780
Abstract
The main functional components of green tea, such as epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC), are found to have a broad antineoplastic activity. The discovery of their targets plays an important role in revealing the antineoplastic mechanism. Therefore, [...] Read more.
The main functional components of green tea, such as epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC), are found to have a broad antineoplastic activity. The discovery of their targets plays an important role in revealing the antineoplastic mechanism. Therefore, to identify potential target proteins for tea polyphenols, we have taken a comparative virtual screening approach using two reverse docking systems, one based on Autodock software and the other on Tarfisdock. Two separate in silico workflows were implemented to derive a set of target proteins related to human diseases and ranked by the binding energy score. Several conventional clinically important proteins with anti-tumor effects are screened out from the PDTD protein database as the potential receptors by both procedures. To further analyze the validity of docking results, we study the binding mode of EGCG and the potential target protein Leukotriene A4 hydrolase in detail. We indicate that interactions mediated by electrostatic and hydrogen bond play a key role in ligand binding. EGCG binds to the enzyme with certain orientation and conformation that is suitable for nucleophilic attacks by several electrical residues inside the enzyme’s activity cavity. This study provides useful information for studying the antitumor mechanism of tea’s functional components. The comparative reverse docking strategy presented generates a tractable set of antineoplastic proteins for future experimental validation as drug targets against tumors. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle
Syntheses and Self-assembling Behaviors of Pentagonal Conjugates of Tryptophane Zipper-Forming Peptide
Int. J. Mol. Sci. 2011, 12(8), 5187-5199; https://doi.org/10.3390/ijms12085187 - 15 Aug 2011
Cited by 9 | Viewed by 5054
Abstract
Pentagonal conjugates of tryptophane zipper-forming peptide (CKTWTWTE) with a pentaazacyclopentadecane core (Pentagonal-Gly-Trpzip and Pentagonal-Ala-Trpzip) were synthesized and their self-assembling behaviors were investigated in water. Pentagonal-Gly-Trpzip self-assembled into nanofibers with the width of about 5 nm in neutral water (pH 7) via formation of [...] Read more.
Pentagonal conjugates of tryptophane zipper-forming peptide (CKTWTWTE) with a pentaazacyclopentadecane core (Pentagonal-Gly-Trpzip and Pentagonal-Ala-Trpzip) were synthesized and their self-assembling behaviors were investigated in water. Pentagonal-Gly-Trpzip self-assembled into nanofibers with the width of about 5 nm in neutral water (pH 7) via formation of tryptophane zipper, which irreversibly converted to nanoribbons by heating. In contrast, Pentagonal-Ala-Trpzip formed irregular aggregates in water. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2011)
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Open AccessReview
Major Histocompatibility Complex (MHC) Markers in Conservation Biology
Int. J. Mol. Sci. 2011, 12(8), 5168-5186; https://doi.org/10.3390/ijms12085168 - 15 Aug 2011
Cited by 64 | Viewed by 8922
Abstract
Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a changing [...] Read more.
Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a changing environment. In this way, loss of genetic polymorphism is linked with extinction risk. Recent advances in sequencing technologies mean that obtaining measures of genetic diversity at functionally important genes is within reach for conservation programs. A key region of the genome that should be targeted for population genetic studies is the Major Histocompatibility Complex (MHC). MHC genes, found in all jawed vertebrates, are the most polymorphic genes in vertebrate genomes. They play key roles in immune function via immune-recognition and -surveillance and host-parasite interaction. Therefore, measuring levels of polymorphism at these genes can provide indirect measures of the immunological fitness of populations. The MHC has also been linked with mate-choice and pregnancy outcomes and has application for improving mating success in captive breeding programs. The recent discovery that genetic diversity at MHC genes may protect against the spread of contagious cancers provides an added impetus for managing and protecting MHC diversity in wild populations. Here we review the field and focus on the successful applications of MHC-typing for conservation management. We emphasize the importance of using MHC markers when planning and executing wildlife rescue and conservation programs but stress that this should not be done to the detriment of genome-wide diversity. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessArticle
Self-Assembly of Protein Monolayers Engineered for Improved Monoclonal Immunoglobulin G Binding
Int. J. Mol. Sci. 2011, 12(8), 5157-5167; https://doi.org/10.3390/ijms12085157 - 15 Aug 2011
Cited by 5 | Viewed by 4786
Abstract
Bacterial outer membrane proteins, along with a filling lipid molecule can be modified to form stable self-assembled monolayers on gold. The transmembrane domain of Escherichia coli outer membrane protein A has been engineered to create a scaffold protein to which functional motifs can [...] Read more.
Bacterial outer membrane proteins, along with a filling lipid molecule can be modified to form stable self-assembled monolayers on gold. The transmembrane domain of Escherichia coli outer membrane protein A has been engineered to create a scaffold protein to which functional motifs can be fused. In earlier work we described the assembly and structure of an antibody-binding array where the Z domain of Staphylococcus aureus protein A was fused to the scaffold protein. Whilst the binding of rabbit polyclonal immunoglobulin G (IgG) to the array is very strong, mouse monoclonal IgG dissociates from the array easily. This is a problem since many immunodiagnostic tests rely upon the use of mouse monoclonal antibodies. Here we describe a strategy to develop an antibody-binding array that will bind mouse monoclonal IgG with lowered dissociation from the array. A novel protein consisting of the scaffold protein fused to two pairs of Z domains separated by a long flexible linker was manufactured. Using surface plasmon resonance the self-assembly of the new protein on gold and the improved binding of mouse monoclonal IgG were demonstrated. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2011)
Open AccessReview
Enhancing Single Molecule Imaging in Optofluidics and Microfluidics
Int. J. Mol. Sci. 2011, 12(8), 5135-5156; https://doi.org/10.3390/ijms12085135 - 12 Aug 2011
Cited by 17 | Viewed by 5800
Abstract
Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal [...] Read more.
Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking. Full article
(This article belongs to the Special Issue Microfluidics)
Open AccessArticle
Alert-QSAR. Implications for Electrophilic Theory of Chemical Carcinogenesis
Int. J. Mol. Sci. 2011, 12(8), 5098-5134; https://doi.org/10.3390/ijms12085098 - 11 Aug 2011
Cited by 31 | Viewed by 5444
Abstract
Given the modeling and predictive abilities of quantitative structure activity relationships (QSARs) for genotoxic carcinogens or mutagens that directly affect DNA, the present research investigates structural alert (SA) intermediate-predicted correlations ASA of electrophilic molecular structures with observed carcinogenic potencies in rats (observed [...] Read more.
Given the modeling and predictive abilities of quantitative structure activity relationships (QSARs) for genotoxic carcinogens or mutagens that directly affect DNA, the present research investigates structural alert (SA) intermediate-predicted correlations ASA of electrophilic molecular structures with observed carcinogenic potencies in rats (observed activity, A = Log[1/TD50], i.e., ASA=f(X1SA,X2SA,...)). The present method includes calculation of the recently developed residual correlation of the structural alert models, i.e., ARASA=f(A-ASA,X1SA,X2SA,...) . We propose a specific electrophilic ligand-receptor mechanism that combines electronegativity with chemical hardness-associated frontier principles, equality of ligand-reagent electronegativities and ligand maximum chemical hardness for highly diverse toxic molecules against specific receptors in rats. The observed carcinogenic activity is influenced by the induced SA-mutagenic intermediate effect, alongside Hansch indices such as hydrophobicity (LogP), polarizability (POL) and total energy (Etot), which account for molecular membrane diffusion, ionic deformation, and stericity, respectively. A possible QSAR mechanistic interpretation of mutagenicity as the first step in genotoxic carcinogenesis development is discussed using the structural alert chemoinformation and in full accordance with the Organization for Economic Co-operation and Development QSAR guidance principles. Full article
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
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Open AccessArticle
Combined 3D-QSAR and Docking Modelling Study on Indolocarbazole Series Compounds as Tie-2 Inhibitors
Int. J. Mol. Sci. 2011, 12(8), 5080-5097; https://doi.org/10.3390/ijms12085080 - 10 Aug 2011
Cited by 7 | Viewed by 3844
Abstract
Tie-2, a kind of endothelial cell tyrosine kinase receptor, is required for embryonic blood vessel development and tumor angiogenesis. Several compounds that showed potent activity toward this attractive anticancer drug target in the assay have been reported. In order to investigate the structure-activity [...] Read more.
Tie-2, a kind of endothelial cell tyrosine kinase receptor, is required for embryonic blood vessel development and tumor angiogenesis. Several compounds that showed potent activity toward this attractive anticancer drug target in the assay have been reported. In order to investigate the structure-activity correlation of indolocarbazole series compounds and modify them to improve their selectivity and activity, 3D-QSAR models were built using CoMFA and CoMSIA methods and molecular docking was used to check the results. Based on the common sketch align, two good QSAR models with high predictabilities (CoMFA model: q2 = 0.823, r2 = 0.979; CoMSIA model: q2 = 0.804, r2 = 0.967) were obtained and the contour maps obtained from both models were applied to identify the influence on the biological activity. Molecular docking was then used to confirm the results. Combined with the molecular docking results, the detail binding mode between the ligands and Tie-2 was elucidated, which enabled us to interpret the structure-activity relationship. These satisfactory results not only offered help to comprehend the action mechanism of indolocarbazole series compounds, but also provide new information for the design of new potent inhibitors. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessReview
Identification and Role of Regulatory Non-Coding RNAs in Listeria monocytogenes
Int. J. Mol. Sci. 2011, 12(8), 5070-5079; https://doi.org/10.3390/ijms12085070 - 10 Aug 2011
Cited by 13 | Viewed by 4467
Abstract
Bacterial regulatory non-coding RNAs control numerous mRNA targets that direct a plethora of biological processes, such as the adaption to environmental changes, growth and virulence. Recently developed high-throughput techniques, such as genomic tiling arrays and RNA-Seq have allowed investigating prokaryotic cis- and [...] Read more.
Bacterial regulatory non-coding RNAs control numerous mRNA targets that direct a plethora of biological processes, such as the adaption to environmental changes, growth and virulence. Recently developed high-throughput techniques, such as genomic tiling arrays and RNA-Seq have allowed investigating prokaryotic cis- and trans-acting regulatory RNAs, including sRNAs, asRNAs, untranslated regions (UTR) and riboswitches. As a result, we obtained a more comprehensive view on the complexity and plasticity of the prokaryotic genome biology. Listeria monocytogenes was utilized as a model system for intracellular pathogenic bacteria in several studies, which revealed the presence of about 180 regulatory RNAs in the listerial genome. A regulatory role of non-coding RNAs in survival, virulence and adaptation mechanisms of L. monocytogenes was confirmed in subsequent experiments, thus, providing insight into a multifaceted modulatory function of RNA/mRNA interference. In this review, we discuss the identification of regulatory RNAs by high-throughput techniques and in their functional role in L. monocytogenes. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
Open AccessArticle
Effect of Cistanches Herba Aqueous Extract on Bone Loss in Ovariectomized Rat
Int. J. Mol. Sci. 2011, 12(8), 5060-5069; https://doi.org/10.3390/ijms12085060 - 08 Aug 2011
Cited by 21 | Viewed by 3740
Abstract
To assess the ability of traditional Chinese medicine Cistanches Herba extract (CHE) to prevent bone loss in the ovariectomized (OVX) rat, Cistanches Herba extract (CHE) was administered intragastrically to the rats. Female rats were anesthetized with pentobarbital sodium (40 mg kg−1, [...] Read more.
To assess the ability of traditional Chinese medicine Cistanches Herba extract (CHE) to prevent bone loss in the ovariectomized (OVX) rat, Cistanches Herba extract (CHE) was administered intragastrically to the rats. Female rats were anesthetized with pentobarbital sodium (40 mg kg−1, i.p.), and their ovaries were removed bilaterally. The rats in the sham-operated group were anesthetized, laparotomized, and sutured without removing their ovaries. After 1 week of recovery from surgery, the OVX rats were randomly divided into three groups and orally treated with H2O (OVX group) or CHE (100 or 200 mg kg−1 daily) for 3 months. The sham-operated group (n = 8) was orally treated with H2O. After 3 months, the total body bone mineral density (BMD), bone mineral content (BMC), Bone biomechanical index, blood mineral levels and blood antioxidant enzymes activities were examined in sham-operated, ovariectomized and Cistanches Herba extract treated rats. Results showed that Cistanches Herba extract treatment significantly dose-dependently enhanced bone mineral density (BMD), bone mineral content (BMC), maximum load, displacement at maximum load, stress at maximum load, load at auto break, displacement at auto break, and stress at auto break, and blood antioxidant enzymes activities, decreased blood Ca, Zn and Cu levels compared to the OVX group. This experiment demonstrates that the administration of Cistanches Herba extract to ovariectomized rats reverses bone loss and prevents osteoporosis. Full article
(This article belongs to the Section Biochemistry)
Open AccessArticle
A Pilot Study of the Association of Tumor Necrosis Factor Alpha Polymorphisms with Psoriatic Arthritis in the Romanian Population
Int. J. Mol. Sci. 2011, 12(8), 5052-5059; https://doi.org/10.3390/ijms12085052 - 08 Aug 2011
Cited by 11 | Viewed by 4667
Abstract
Tumor necrosis factor alpha (TNF-alpha) is an important pro-inflammatory cytokine implicated in the pathogenesis of psoriatic arthritis. We have performed a case-control association study of three TNF-alpha gene polymorphisms in a group of Romanian psoriatic arthritis patients versus ethnically matched controls. A second [...] Read more.
Tumor necrosis factor alpha (TNF-alpha) is an important pro-inflammatory cytokine implicated in the pathogenesis of psoriatic arthritis. We have performed a case-control association study of three TNF-alpha gene polymorphisms in a group of Romanian psoriatic arthritis patients versus ethnically matched controls. A second group of patients with undifferentiated spondyloarthritis was used in order to look for similarities in the genetic background of the two rheumatic disorders. The −857C/T polymorphism was associated with susceptibility to psoriatic arthritis in our population at the individual level (p = 0.03, OR 1.65, 95% CI 1.05–2.57) and in combined haplotypes with the −238G/A and −308G/A SNPs. Regarding the investigated polymorphisms and derived haplotypes, no potential association was found with the susceptibility to undifferentiated spondyloarthritis in Romanian patients. Full article
(This article belongs to the Section Biochemistry)
Open AccessArticle
Potential Antibacterial Activity of Carvacrol-Loaded Poly(DL-lactide-co-glycolide) (PLGA) Nanoparticles against Microbial Biofilm
Int. J. Mol. Sci. 2011, 12(8), 5039-5051; https://doi.org/10.3390/ijms12085039 - 08 Aug 2011
Cited by 85 | Viewed by 6430
Abstract
The ability to form biofilms contributes significantly to the pathogenesis of many microbial infections, including a variety of ocular diseases often associated with the biofilm formation on foreign materials. Carvacrol (Car.) is an important component of essential oils and recently has attracted much [...] Read more.
The ability to form biofilms contributes significantly to the pathogenesis of many microbial infections, including a variety of ocular diseases often associated with the biofilm formation on foreign materials. Carvacrol (Car.) is an important component of essential oils and recently has attracted much attention pursuant to its ability to promote microbial biofilm disruption. In the present study Car. has been encapsulated in poly(DL-lactide-co-glycolide (PLGA) nanocapsules in order to obtain a suitable drug delivery system that could represent a starting point for developing new therapeutic strategies against biofilm-associated infections, such as improving the drug effect by associating an antimicrobial agent with a biofilm viscoelasticity modifier. Full article
(This article belongs to the Section Materials Science)
Open AccessArticle
Comparative Clinical Study of Bactigras and Telfa AMD for Skin Graft Donor-Site Dressing
Int. J. Mol. Sci. 2011, 12(8), 5031-5038; https://doi.org/10.3390/ijms12085031 - 08 Aug 2011
Cited by 16 | Viewed by 4551
Abstract
The Bactigras® paraffin tulle coated with chlorhexidine is normally used for the treatment of donor-site wounds in burn patients who received split-thickness skin grafts in several centers. It has some disadvantages, such as adhesion to wound surfaces and pain from the irritation [...] Read more.
The Bactigras® paraffin tulle coated with chlorhexidine is normally used for the treatment of donor-site wounds in burn patients who received split-thickness skin grafts in several centers. It has some disadvantages, such as adhesion to wound surfaces and pain from the irritation caused by this dressing. The Telfa AMD®, a non-adherent wound dressing which consists of absorbent cotton fibers impregnated with polyhexamethylene biguanide enclosed in a sleeve of thermoplastic polymers, is a new option for donor-site wound care which causes less adherence to the wound. The purpose of this study was to compare clinical efficacy of these two dressings for the management of donor-site wounds. Thirty-two patients who received split-thickness skin grafts by donor site harvesting from the thigh were enrolled in this study and randomized into two groups receiving either the Bactigras® or the Telfa AMD® wound treatment. Re-epithelialization, pain, infection and cost-effectiveness analyses were compared between both groups. The results showed that there was no significant difference in age, area of donor sites or length of hospital stays between the groups (p > 0.05). However, the day of re-epithelialization (≥90%) was significantly shorter in patients treated with the Telfa AMD® compared to the Bactigras® group (14.00 ± 3.05 vs. 9.25 ± 1.88 days for Bactigras® and Telfa AMD® groups, respectively, p < 0.001). The average pain score was also significantly lower in the Telfa AMD® group (1.57 ± 0.55 vs. 4.70 ± 1.16, p < 0.001). There was no difference in the cost of treatment between the groups (4.64 ± 1.97 vs. 5.72 ± 2.54 USD, p = 0.19). This study indicated that the Telfa AMD® was an effective dressing for the treatment of donor-site wounds. Full article
(This article belongs to the Section Materials Science)
Open AccessArticle
Investigation of the Structure Requirement for 5-HT6 Binding Affinity of Arylsulfonyl Derivatives: A Computational Study
Int. J. Mol. Sci. 2011, 12(8), 5011-5030; https://doi.org/10.3390/ijms12085011 - 08 Aug 2011
Cited by 12 | Viewed by 3734
Abstract
5-HT6 receptor has been implicated in a series of diseases including anxiety, depression, schizophrenia and cognitive dysfunctions. 5-HT6 ligands have been reported to play a significant role in the treatment for central nervous system (CNS) diseases. Presently, a large series of [...] Read more.
5-HT6 receptor has been implicated in a series of diseases including anxiety, depression, schizophrenia and cognitive dysfunctions. 5-HT6 ligands have been reported to play a significant role in the treatment for central nervous system (CNS) diseases. Presently, a large series of 223 5-HT6 ligands were studied using a combinational method by 3D-QSAR, molecular docking and molecular dynamics calculations for further improvement of potency. The optimal 3D models exhibit satisfying statistical results with r2ncv, q2 values of 0.85 and 0.50 for CoMFA, 0.81 and 0.53 for CoMSIA, respectively. Their predictive powers were validated by external test set, showing r2pred of 0.71 and 0.76. The contour maps also provide a visual representation of contributions of steric, electrostatic, hydrophobic and hydrogen bond fields as well as the prospective binding models. In addition, the agreement between 3D-QSAR, molecular docking and molecular dynamics simulation proves the rationality of the developed models. These results, we hope, may be helpful in designing novel and potential 5-HT6 ligands. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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