International Journal of Molecular Sciences

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Open AccessReview

Molecular Basis for Chiral Selection in RNA Aminoacylation

by Koji Tamura

Int. J. Mol. Sci. 2011, 12(7), 4745-4757; https://doi.org/10.3390/ijms12074745 - 22 Jul 2011

Cited by 20 | Viewed by 10464

The chiral-selective aminoacylation of an RNA minihelix is a potential progenitor to modern tRNA-based protein synthesis using l-amino acids. This article describes the molecular basis for this chiral selection. The extended double helical form of an RNA minihelix with a CCA triplet (acceptor [...] Read more.

The chiral-selective aminoacylation of an RNA minihelix is a potential progenitor to modern tRNA-based protein synthesis using l-amino acids. This article describes the molecular basis for this chiral selection. The extended double helical form of an RNA minihelix with a CCA triplet (acceptor of an amino acid), an aminoacyl phosphate donor nucleotide (mimic of aminoacyl-AMP), and a bridging nucleotide facilitates chiral-selective aminoacylation. Energetically, the reaction is characterized by a downhill reaction wherein an amino acid migrates from a high-energy acyl phosphate linkage to a lower-energy carboxyl ester linkage. The reaction occurs under the restriction that the nucleophilic attack of O, from 3′-OH in the terminal CCA, to C, from C=O in the acyl phosphate linkage, must occur at a Bürgi-Dunitz angle, which is defined as the O–C=O angle of approximately 105°. The extended double helical form results in a steric hindrance at the side chain of the amino acid leading to chiral preference combined with cation coordinations in the amino acid and the phosphate oxygen. Such a system could have developed into the protein biosynthetic system with an exclusively chiral component (l-amino acids) via (proto) ribosomes. Full article

(This article belongs to the Special Issue Origin of Life 2011)

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Open AccessArticle

Antifungal Activity of Denture Soft Lining Material Modified by Silver Nanoparticles—A Pilot Study

by Grzegorz Chladek, Anna Mertas, Izabela Barszczewska-Rybarek, Teresa Nalewajek, Jarosław Żmudzki, Wojciech Król and Jan Łukaszczyk

Int. J. Mol. Sci. 2011, 12(7), 4735-4744; https://doi.org/10.3390/ijms12074735 - 22 Jul 2011

Cited by 87 | Viewed by 12592

Abstract

Soft liner materials in oral cavity environments are easily colonized both by fungi and dental plaque. These factors are the cause of mucosal infections. The microorganism that most frequently colonizes soft liner materials is Candida albicans. Colonization occurs on the surface of [...] Read more.

Soft liner materials in oral cavity environments are easily colonized both by fungi and dental plaque. These factors are the cause of mucosal infections. The microorganism that most frequently colonizes soft liner materials is Candida albicans. Colonization occurs on the surface of materials and within materials. A solution to this problem might involve modification of soft liner materials with silver nanoparticles (AgNPs). In this article, we present results showing the antifungal efficacy of silicone soft lining materials modified with AgNPs. The modification process was conducted by dissolving both material components (base and catalyst) in a colloidal solution of AgNPs and evaporating the solvent. Composites with various AgNP concentrations (10, 20, 40, 80, 120 and 200 ppm) were examined. The in vitro antifungal efficacy (AFE) of composite samples was 16.3% to 52.5%. Full article

(This article belongs to the Special Issue Dental Materials)

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Open AccessArticle

Microcystin-LR Induces Apoptosis via NF-κB /iNOS Pathway in INS-1 Cells

by Yong Ji, Gao Lu, Guoqiang Chen, Bin Huang, Xian Zhang, Kai Shen and Song Wu

Int. J. Mol. Sci. 2011, 12(7), 4722-4734; https://doi.org/10.3390/ijms12074722 - 22 Jul 2011

Cited by 44 | Viewed by 9476

Abstract

Cyanobacterial toxins, especially the microcystins, are found in eutrophied waters throughout the world, and their potential to impact on human and animal health is a cause for concern. Microcystin-LR (MC-LR) is one of the common toxic microcystin congeners and occurs frequently in diverse [...] Read more.

Cyanobacterial toxins, especially the microcystins, are found in eutrophied waters throughout the world, and their potential to impact on human and animal health is a cause for concern. Microcystin-LR (MC-LR) is one of the common toxic microcystin congeners and occurs frequently in diverse water systems. Recent work suggested that apoptosis plays a major role in the toxic effects induced by MC-LR in hepatocytes. However, the roles of MC-LR in pancreatic beta cells have not been fully established. The aim of the present study was to assess possible in vitro effects of MC-LR on cell apoptosis in the rat insulinoma cell line, INS-1. Our results demonstrated that MC-LR promoted selectively activation of NF-κB (increasing nuclear p50/p65 translocation) and increased the mRNA and protein levels of induced nitric oxide synthase (iNOS). The chronic treatment with MC-LR stimulated nitric oxide (NO) production derived from iNOS and induced apoptosis in a dose dependent manner in INS-1 cells. Meanwhile, this effect was inhibited by the NF-κB inhibitor PDTC, which reversed the apoptosis induced by MC-LR. Our observations indicate that MC-LR induced cell apoptosis via an iNOS-dependent pathway. A well-known nuclear transcription factor, NF-κB, is activated and mediates intracellular nitric oxide synthesis. We suggest that the apoptosis induced by chronic MC-LR in vivo presents a possible cause of β-cell dysfunction, as a key environmental factor in the development of diabetes mellitus. Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Epigenetics: New Questions on the Response to Hypoxia

by Joel I. Perez-Perri, Julieta M. Acevedo and Pablo Wappner

Int. J. Mol. Sci. 2011, 12(7), 4705-4721; https://doi.org/10.3390/ijms12074705 - 21 Jul 2011

Cited by 62 | Viewed by 10753

Abstract

Reduction in oxygen levels below normal concentrations plays important roles in different normal and pathological conditions, such as development, tumorigenesis, chronic kidney disease and stroke. Organisms exposed to hypoxia trigger changes at both cellular and systemic levels to recover oxygen homeostasis. Most of [...] Read more.

Reduction in oxygen levels below normal concentrations plays important roles in different normal and pathological conditions, such as development, tumorigenesis, chronic kidney disease and stroke. Organisms exposed to hypoxia trigger changes at both cellular and systemic levels to recover oxygen homeostasis. Most of these processes are mediated by Hypoxia Inducible Factors, HIFs, a family of transcription factors that directly induce the expression of several hundred genes in mammalian cells. Although different aspects of HIF regulation are well known, it is still unclear by which precise mechanism HIFs activate transcription of their target genes. Concomitantly, hypoxia provokes a dramatic decrease of general transcription that seems to rely in part on epigenetic changes through a poorly understood mechanism. In this review we discuss the current knowledge on chromatin changes involved in HIF dependent gene activation, as well as on other epigenetic changes, not necessarily linked to HIF that take place under hypoxic conditions. Full article

(This article belongs to the Special Issue Chromatin Assembly)

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Open AccessArticle

Vma8p-GFP Fusions Can Be Functionally Incorporated into V-ATPase, Suggesting Structural Flexibility at the Top of V₁

by Szczepan Nowakowski, Dalibor Mijaljica, Mark Prescott and Rodney J. Devenish

Int. J. Mol. Sci. 2011, 12(7), 4693-4704; https://doi.org/10.3390/ijms12074693 - 20 Jul 2011

Cited by 2 | Viewed by 7184

Abstract

The vacuolar ATPase (V-ATPase) complex of yeast (Saccharomyces cerevisiae) is comprised of two sectors, V₁ (catalytic) and V_O (proton transfer). The hexameric (A₃B₃) cylinder of V₁ has a central cavity that must accommodate at [...] Read more.

The vacuolar ATPase (V-ATPase) complex of yeast (Saccharomyces cerevisiae) is comprised of two sectors, V₁ (catalytic) and V_O (proton transfer). The hexameric (A₃B₃) cylinder of V₁ has a central cavity that must accommodate at least part of the rotary stalk of V-ATPase, a key component of which is subunit D (Vma8p). Recent electron microscopy (EM) data for the prokaryote V-ATPase complex (Thermus thermophilus) suggest that subunit D penetrates deeply into the central cavity. The functional counterpart of subunit D in mitochondrial F₁F_O-ATP synthase, subunit γ, occupies almost the entire length of the central cavity. To test whether the structure of yeast Vma8p mirrors that of subunit g, we probed the location of the C-terminus of Vma8p by attachment of a large protein adduct, green fluorescent protein (GFP). We found that truncated Vma8p proteins lacking up to 40 C-terminal residues fused to GFP can be incorporated into functional V-ATPase complexes, and are able to support cell growth under alkaline conditions. We conclude that large protein adducts can be accommodated at the top of the central cavity of V₁ without compromising V-ATPase function, arguing for structural flexibility of the V₁ sector. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Effect of Freeze-Drying on the Antioxidant Compounds and Antioxidant Activity of Selected Tropical Fruits

by Norshahida Mohamad Shofian, Azizah Abdul Hamid, Azizah Osman, Nazamid Saari, Farooq Anwar, Mohd Sabri Pak Dek and Muhammad Redzuan Hairuddin

Int. J. Mol. Sci. 2011, 12(7), 4678-4692; https://doi.org/10.3390/ijms12074678 - 20 Jul 2011

Cited by 203 | Viewed by 19481

Abstract

The effects of freeze-drying on antioxidant compounds and antioxidant activity of five tropical fruits, namely starfruit (Averrhoa carambola L.), mango (Mangifera indica L.), papaya (Carica papaya L.), muskmelon (Cucumis melo L.), and watermelon Citruluss lanatus (Thunb.) were investigated. Significant [...] Read more.

The effects of freeze-drying on antioxidant compounds and antioxidant activity of five tropical fruits, namely starfruit (Averrhoa carambola L.), mango (Mangifera indica L.), papaya (Carica papaya L.), muskmelon (Cucumis melo L.), and watermelon Citruluss lanatus (Thunb.) were investigated. Significant (p < 0.05) differences, for the amounts of total phenolic compounds (TPC), were found between the fresh and freeze-dried fruit samples, except muskmelon. There was no significant (p > 0.05) change, however, observed in the ascorbic acid content of the fresh and freeze-dried fruits. Similarly, freeze-drying did not exert any considerable effect on β-carotene concentration of fruits, except for mango and watermelon, where significantly (p < 0.05) higher levels were detected in the fresh samples. The results of DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging and reducing power assays revealed that fresh samples of starfruit and mango had relatively higher antioxidant activity. In case of linoleic acid peroxidation inhibition measurement, a significant (p < 0.05) but random variation was recorded between the fresh and freeze-dried fruits. Overall, in comparison to β-carotene and ascorbic acid, a good correlation was established between the result of TPC and antioxidant assays, indicating that phenolics might have been the dominant compounds contributing towards the antioxidant activity of the fruits tested. Full article

(This article belongs to the Section Biochemistry)

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Sida rhomboidea. Roxb Leaf Extract Down-Regulates Expression of PPARγ2 and Leptin Genes in High Fat Diet Fed C57BL/6J Mice and Retards in Vitro 3T3L1 Pre-Adipocyte Differentiation

by Menaka C. Thounaojam, Ravirajsinh N. Jadeja, Umed V. Ramani, Ranjitsinh V. Devkar and A. V. Ramachandran

Int. J. Mol. Sci. 2011, 12(7), 4661-4677; https://doi.org/10.3390/ijms12074661 - 19 Jul 2011

Cited by 19 | Viewed by 11954

Abstract

Sida rhomboidea. Roxb leaf extract (SRLE) is being used by the populace of North-East India to alleviate symptoms of diabetes and obesity. We have previously reported its hypolipidemic and anti-diabetic properties. In this study, we report the effect of SRLE on (i) [...] Read more.

Sida rhomboidea. Roxb leaf extract (SRLE) is being used by the populace of North-East India to alleviate symptoms of diabetes and obesity. We have previously reported its hypolipidemic and anti-diabetic properties. In this study, we report the effect of SRLE on (i) in vivo modulation of genes controlling high fat diet (HFD) induced obesity and (ii) in vitro 3T3L1 pre-adipocyte differentiation and leptin release. Supplementation with SRLE significantly prevented HFD induced increment in bodyweight, plasma lipids and leptin, visceral adiposity and adipocyte hypertrophy. Also, SRLE supplementation reduced food intake, down regulated PPARγ2, SREBP1c, FAS and LEP expressions and up-regulated CPT-1 in epididymal adipose tissue compared to obese mice. In vitro adipogenesis of 3T3L1 pre-adipocytes was significantly retarded in the presence of SRLE extract. Also decreased triglyceride accumulation, leptin release and glyceraldehyde-3-Phosphate dehydrogenase activity along with higher glycerol release without significant alteration of viability of 3T3L1 pre-adipocytes, was recorded. Our findings suggest that prevention of HFD induced visceral adiposity is primarily by down regulation of PPARγ2 and leptin gene expression coupled with attenuation of food intake in C57BL/6J mice. SRLE induced prevention of pre-adipocytes differentiation, and leptin release further substantiated these findings and scientifically validates the potential application of SRLE as a therapeutic agent against obesity. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Chitosan Interaction with Iron from Yoghurt Using an In Vitro Digestive Model: Comparative Study with Plant Dietary Fibers

by Marina Dello Staffolo, Miriam Martino, Alicia Bevilacqua, Mirta Montero, María Susana Rodríguez and Liliana Albertengo

Int. J. Mol. Sci. 2011, 12(7), 4647-4660; https://doi.org/10.3390/ijms12074647 - 19 Jul 2011

Cited by 11 | Viewed by 9969

Abstract

The objective of this work was to investigate the interaction of chitosan with iron from yoghurt by an in vitro gastrointestinal tract model. Taking into account that chitosan is a polysaccharide included in fiber definition by Codex Alimentarius; chitosan behavior was studied and [...] Read more.

The objective of this work was to investigate the interaction of chitosan with iron from yoghurt by an in vitro gastrointestinal tract model. Taking into account that chitosan is a polysaccharide included in fiber definition by Codex Alimentarius; chitosan behavior was studied and compared with different plant fiber (wheat, bamboo, apple, psyllium and inulin) behaviors, in the same in vitro conditions. Ferrous sulfate was added to yoghurts with each type of fiber. The gastric environment was simulated with HCl (pH 1.0–2.0). The duodenal environment was simulated with NaHCO₃ (pH 6.8–7.2) and a dialysis tubing cellulose membrane. Results showed that chitosan had the highest iron retention percentages (53.2% at 30 min; 56.8% at 60 min) interacting in a more pronounced manner with iron than the plant fibers used in this work. Full article

(This article belongs to the Special Issue Dietary Fibre: Biochemistry and Nutritional Science)

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Open AccessArticle

Enhanced Chiral Recognition by Cyclodextrin Dimers

by Jens Voskuhl, Kira Schaepe and Bart Jan Ravoo

Int. J. Mol. Sci. 2011, 12(7), 4637-4646; https://doi.org/10.3390/ijms12074637 - 18 Jul 2011

Cited by 10 | Viewed by 8959

Abstract

In this article we investigate the effect of multivalency in chiral recognition. To this end, we measured the host-guest interaction of a β-cyclodextrin dimer with divalent chiral guests. We report the synthesis of carbohydrate-based water soluble chiral guests functionalized with two borneol, menthol, [...] Read more.

In this article we investigate the effect of multivalency in chiral recognition. To this end, we measured the host-guest interaction of a β-cyclodextrin dimer with divalent chiral guests. We report the synthesis of carbohydrate-based water soluble chiral guests functionalized with two borneol, menthol, or isopinocampheol units in either (+) or (–) configuration. We determined the interaction of these divalent guests with a β-cyclodextrin dimer using isothermal titration calorimetry. It was found that—in spite of a highly unfavorable conformation—the cyclodextrin dimer binds to guest dimers with an increased enantioselectivity, which clearly reflects the effect of multivalency. Full article

(This article belongs to the Special Issue Molecular Self-Assembly 2011)

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Open AccessArticle

Acid-Denatured Green Fluorescent Protein (GFP) as Model Substrate to Study the Chaperone Activity of Protein Disulfide Isomerase

by Rosa E. Mares, Samuel G. Meléndez-López and Marco A. Ramos

Int. J. Mol. Sci. 2011, 12(7), 4625-4636; https://doi.org/10.3390/ijms12074625 - 18 Jul 2011

Cited by 18 | Viewed by 10781

Abstract

Green fluorescent protein (GFP) has been widely used in several molecular and cellular biology applications, since it is remarkably stable in vitro and in vivo. Interestingly, native GFP is resistant to the most common chemical denaturants; however, a low fluorescence signal has [...] Read more.

Green fluorescent protein (GFP) has been widely used in several molecular and cellular biology applications, since it is remarkably stable in vitro and in vivo. Interestingly, native GFP is resistant to the most common chemical denaturants; however, a low fluorescence signal has been observed after acid-induced denaturation. Furthermore, this acid-denatured GFP has been used as substrate in studies of the folding activity of some bacterial chaperones and other chaperone-like molecules. Protein disulfide isomerase enzymes, a family of eukaryotic oxidoreductases that catalyze the oxidation and isomerization of disulfide bonds in nascent polypeptides, play a key role in protein folding and it could display chaperone activity. However, contrasting results have been reported using different proteins as model substrates. Here, we report the further application of GFP as a model substrate to study the chaperone activity of protein disulfide isomerase (PDI) enzymes. Since refolding of acid-denatured GFP can be easily and directly monitored, a simple micro-assay was used to study the effect of the molecular participants in protein refolding assisted by PDI. Additionally, the effect of a well-known inhibitor of PDI chaperone activity was also analyzed. Because of the diversity their functional activities, PDI enzymes are potentially interesting drug targets. Since PDI may be implicated in the protection of cells against ER stress, including cancer cells, inhibitors of PDI might be able to enhance the efficacy of cancer chemotherapy; furthermore, it has been demonstrated that blocking the reductive cleavage of disulfide bonds of proteins associated with the cell surface markedly reduces the infectivity of the human immunodeficiency virus. Although several high-throughput screening (HTS) assays to test PDI reductase activity have been described, we report here a novel and simple micro-assay to test the chaperone activity of PDI enzymes, which is amenable for HTS of PDI inhibitors. Full article

(This article belongs to the Special Issue Protein Folding 2011)

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Open AccessArticle

Identification and Categorization of Liver Toxicity Markers Induced by a Related Pair of Drugs

by Ching-Wei Chang, Frederick A. Beland, Wade M. Hines, James C. Fuscoe, Tao Han and James J. Chen

Int. J. Mol. Sci. 2011, 12(7), 4609-4624; https://doi.org/10.3390/ijms12074609 - 15 Jul 2011

Cited by 10 | Viewed by 8351

Abstract

Drug-induced liver injury (DILI) is the primary adverse event that results in the withdrawal of drugs from the market and a frequent reason for the failure of drug candidates in the pre-clinical or clinical phases of drug development. This paper presents an approach [...] Read more.

Drug-induced liver injury (DILI) is the primary adverse event that results in the withdrawal of drugs from the market and a frequent reason for the failure of drug candidates in the pre-clinical or clinical phases of drug development. This paper presents an approach for identifying potential liver toxicity genomic biomarkers from a liver toxicity biomarker study involving the paired compounds entacapone (“non-liver toxic drug”) and tolcapone (“hepatotoxic drug”). Molecular analysis of the rat liver and plasma samples, combined with statistical analysis, revealed many similarities and differences between the in vivo biochemical effects of the two drugs. Six hundred and ninety-five genes and 61 pathways were selected based on the classification scheme. Of the 61 pathways, 5 were specific to treatment with tolcapone. Two of the 12 animals in the tolcapone group were found to have high ALT, AST, or TBIL levels. The gene Vars2 (valyl-tRNA synthetase 2) was identified in both animals and the pathway to which it belongs, the aminoacyl-tRNA biosynthesis pathway, was one of the three most significant tolcapone-specific pathways identified. Full article

(This article belongs to the Special Issue Toxicogenomics)

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Open AccessArticle

Enhanced Anti-Tumoral Activity of Methotrexate-Human Serum Albumin Conjugated Nanoparticles by Targeting with Luteinizing Hormone-Releasing Hormone (LHRH) Peptide

by Azade Taheri, Rassoul Dinarvand, Fatemeh Atyabi, Fatemeh Ahadi, Farank Salman Nouri, Mohammad Hossein Ghahremani, Seyed Nasser Ostad, Atefeh Taheri Borougeni and Pooria Mansoori

Int. J. Mol. Sci. 2011, 12(7), 4591-4608; https://doi.org/10.3390/ijms12074591 - 15 Jul 2011

Cited by 47 | Viewed by 10055

Abstract

Active targeting could increase the efficacy of anticancer drugs. Methotrexate-human serum albumin (MTX-HSA) conjugates, functionalized by luteinizing hormone-releasing hormone (LHRH) as targeting moieties, with the aim of specifically targeting the cancer cells, were prepared. Owing to the high expression of LHRH receptors in [...] Read more.

Active targeting could increase the efficacy of anticancer drugs. Methotrexate-human serum albumin (MTX-HSA) conjugates, functionalized by luteinizing hormone-releasing hormone (LHRH) as targeting moieties, with the aim of specifically targeting the cancer cells, were prepared. Owing to the high expression of LHRH receptors in many cancer cells as compared to normal cells, LHRH was used as the targeting ligand in this study. LHRH was conjugated to MTX-HSA nanoparticles via a cross-linker. Three types of LHRH targeted nanoparticles with a mean particle size between 120–138 nm were prepared. The cytotoxicity of LHRH targeted and non-targeted nanoparticles were determined on the LHRH positive and negative cell lines. The internalization of the targeted and non-targeted nanoparticles in LHRH receptor positive and negative cells was investigated using flow cytometry analysis and fluorescence microscopy. The cytotoxicity of the LHRH targeted nanoparticles on the LHRH receptor positive cells were significantly more than non-targeted nanoparticles. LHRH targeted nanoparticles were also internalized by LHRH receptor positive cells significantly more than non-targeted nanoparticles. There were no significant differences between the uptake of targeted and non-targeted nanoparticles to the LHRH receptor negative cells. The active targeting procedure using LHRH targeted MTX-HSA nanoparticles could increase the anti-tumoral activity of MTX. Full article

(This article belongs to the Special Issue Bioactive Nanoparticles (special issue))

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Open AccessArticle

Variations of Antioxidant Properties and NO Scavenging Abilities during Fermentation of Tea

by Yang Xu, Hang Zhao, Min Zhang, Chun-Jie Li, Xue-Zhen Lin, Jun Sheng and Wei Shi

Int. J. Mol. Sci. 2011, 12(7), 4574-4590; https://doi.org/10.3390/ijms12074574 - 15 Jul 2011

Cited by 33 | Viewed by 10058

Abstract

Tea is known as one of the most popular beverages in the world, which is believed to be beneficial for health. The main components in tea will change a lot depending on the different processes of fermentation, and thus the effects of different [...] Read more.

Tea is known as one of the most popular beverages in the world, which is believed to be beneficial for health. The main components in tea will change a lot depending on the different processes of fermentation, and thus the effects of different teas on human health may differ. The aim of this study is to explore the varied abilities of reactive oxygen species (ROS) and nitric oxide (NO) scavenging during the fermentation of tea. In this study, we conducted the in vitro experiments which involved some reaction systems indicating the abilities of scavenging ROS and NO. We also investigated the effects of tea and their components (catechins, theabrownins, caffeine) on the intracellular levels of ROS and NO, using Raw 264.7 cells as the model. We found that regardless of whether it was out of cell system or in Raw 264.7 cells, the abilities of scavenging ROS would decrease during the fermentation of tea. Further, the post-fermented pu-erh tea showed the best effect on inhibiting the lipopolysaccharide (LPS)-induced production of NO. These findings indicated that the fermentation process caused a change of the components which might be due to the changes of their antioxidant properties and NO scavenging abilities. Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Bioactivities from Marine Algae of the Genus Gracilaria

by Cynthia Layse F. De Almeida, Heloina De S. Falcão, Gedson R. De M. Lima, Camila De A. Montenegro, Narlize S. Lira, Petrônio F. De Athayde-Filho, Luis C. Rodrigues, Maria de Fátima V. De Souza, José M. Barbosa-Filho and Leônia M. Batista

Int. J. Mol. Sci. 2011, 12(7), 4550-4573; https://doi.org/10.3390/ijms12074550 - 15 Jul 2011

Cited by 209 | Viewed by 22195

Abstract

Seaweeds are an important source of bioactive metabolites for the pharmaceutical industry in drug development. Many of these compounds are used to treat diseases like cancer, acquired immune-deficiency syndrome (AIDS), inflammation, pain, arthritis, as well as viral, bacterial, and fungal infections. This paper [...] Read more.

Seaweeds are an important source of bioactive metabolites for the pharmaceutical industry in drug development. Many of these compounds are used to treat diseases like cancer, acquired immune-deficiency syndrome (AIDS), inflammation, pain, arthritis, as well as viral, bacterial, and fungal infections. This paper offers a survey of the literature for Gracilaria algae extracts with biological activity, and identifies avenues for future research. Nineteen species of this genus that were tested for antibacterial, antiviral, antifungal, antihypertensive, cytotoxic, spermicidal, embriotoxic, and anti-inflammatory activities are cited from the 121 references consulted. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Variations in Content and Extractability of Durum Wheat (Triticum turgidum L. var durum) Arabinoxylans Associated with Genetic and Environmental Factors

by Roberto Ciccoritti, Giulia Scalfati, Alessandro Cammerata and Daniela Sgrulletta

Int. J. Mol. Sci. 2011, 12(7), 4536-4549; https://doi.org/10.3390/ijms12074536 - 15 Jul 2011

Cited by 31 | Viewed by 8718

Abstract

Arabinoxylans (AX) represent the most abundant components of non-starch polysaccharides in wheat, constituting about 70% of cell wall polysaccharides. An important property of AX is their ability to form highly viscous water solutions; this peculiarity has a significant impact on the technological characteristics [...] Read more.

Arabinoxylans (AX) represent the most abundant components of non-starch polysaccharides in wheat, constituting about 70% of cell wall polysaccharides. An important property of AX is their ability to form highly viscous water solutions; this peculiarity has a significant impact on the technological characteristics of wheat and determines the physiologically positive influence in consumption. Durum wheat (Triticum turgidum L. var durum), the raw material for pasta production, is one of the most important crops in Italy. As part of a large project aimed at improving durum wheat quality, the characterization of the nutritional and technological aspects of whole grains was considered. Particular attention was addressed to identify the best suited genotypes for the production of innovative types of pasta with enhanced functional and organoleptic properties. The objective of the present study was to investigate the genetic variability of AX by examining a group of durum wheat genotypes collected at two localities in Italy for two consecutive years. The environmental influence on AX content and extractability was also evaluated. Variability in the AX fraction contents was observed; the results indicated that AX fractions of durum wheat grain can be affected by the genotype and environment characteristics and the different contribution of genotype and environment to total variation was evidenced. The genotype × environment (G × E) interaction was significant for all examined traits, the variations due to G × E being lower than that of genotype or environment. The data and the statistical analysis allowed identification of the Italian durum wheat varieties that were consistently higher in total arabinoxilans; in addition, principal component analysis biplots illustrated that for arabinoxylan fractions some varieties responded differently in various environment climatic conditions. Full article

(This article belongs to the Special Issue Dietary Fibre: Biochemistry and Nutritional Science)

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Open AccessArticle

Antiviral Activity and Mechanism of Action of Novel Thiourea Containing Chiral Phosphonate on Tobacco Mosaic Virus

by Huitao Fan, Baoan Song, Pinaki S. Bhadury, Linhong Jin, Deyu Hu and Song Yang

Int. J. Mol. Sci. 2011, 12(7), 4522-4535; https://doi.org/10.3390/ijms12074522 - 13 Jul 2011

Cited by 61 | Viewed by 9522

Abstract

Using half-leaf method O,O’-diisopropyl (3-(L-1-(benzylamino)-1-oxo-3-phenylpropan-2-yl)thioureido)(phenyl)methyl phosphonate (2009104) was studied for its activity on tobacco mosaic virus (TMV). It showed good curative activity in vivo and the curative activity at 500 μg/mL was found to be 53.3%. In vivo treatment with the control [...] Read more.

Using half-leaf method O,O’-diisopropyl (3-(L-1-(benzylamino)-1-oxo-3-phenylpropan-2-yl)thioureido)(phenyl)methyl phosphonate (2009104) was studied for its activity on tobacco mosaic virus (TMV). It showed good curative activity in vivo and the curative activity at 500 μg/mL was found to be 53.3%. In vivo treatment with the control agent Ningnanmycin at 500 μg/mL resulted in 51.2% inhibition and curative inhibition rates respectively. Dot-ELISA test was employed to verify the efficacy of activity of compound 200910 for anti-TMV activity. The mechanism of action of compound 2009104 to resist TMV was also studied. The results showed that the resistance enzymes PAL, POD, SOD activity and chlorophyll content after TMV inoculation K₃₂₆ (Nicotiana tabacum K₃₂₆) of tobacco plants followed by treatment with compound 2009104 were significantly enhanced. The study of the effect of compound 2009104 on TMV capsid protein (CP) showed that it inhibited the polymerization process of TMV-CP in vitro. Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Putative Biomarkers and Targets of Estrogen Receptor Negative Human Breast Cancer

by Ziad J. Sahab, Yan-Gao Man, Stephen W. Byers and Qing-Xiang A. Sang

Int. J. Mol. Sci. 2011, 12(7), 4504-4521; https://doi.org/10.3390/ijms12074504 - 13 Jul 2011

Cited by 13 | Viewed by 9684

Abstract

Breast cancer is a progressive and potentially fatal disease that affects women of all ages. Like all progressive diseases, early and reliable diagnosis is the key for successful treatment and annihilation. Biomarkers serve as indicators of pathological, physiological, or pharmacological processes. Her2/neu, CA15.3, [...] Read more.

Breast cancer is a progressive and potentially fatal disease that affects women of all ages. Like all progressive diseases, early and reliable diagnosis is the key for successful treatment and annihilation. Biomarkers serve as indicators of pathological, physiological, or pharmacological processes. Her2/neu, CA15.3, estrogen receptor (ER), progesterone receptor (PR), and cytokeratins are biomarkers that have been approved by the Food and Drug Administration for disease diagnosis, prognosis, and therapy selection. The structural and functional complexity of protein biomarkers and the heterogeneity of the breast cancer pathology present challenges to the scientific community. Here we review estrogen receptor-related putative breast cancer biomarkers, including those of putative breast cancer stem cells, a minor population of estrogen receptor negative tumor cells that retain the stem cell property of self renewal. We also review a few promising cytoskeleton targets for ER alpha negative breast cancer. Full article

(This article belongs to the Special Issue Biomarkers 2011)

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Open AccessArticle

Steady State–Hopf Mode Interactions at the Onset of Electroconvection in the Nematic Liquid Crystal Phase V

by Gyanu Acharya, Gerhard Dangelmayr, James Gleeson and Iuliana Oprea

Int. J. Mol. Sci. 2011, 12(7), 4488-4503; https://doi.org/10.3390/ijms12074488 - 13 Jul 2011

Cited by 3 | Viewed by 6673

Abstract

We report on a new mode interaction found in electroconvection experiments on the nematic liquid crystal mixture Phase V in planar geometry. The mode interaction (codimension two) point occurs at a critical value of the frequency of the driving AC voltage. For frequencies [...] Read more.

We report on a new mode interaction found in electroconvection experiments on the nematic liquid crystal mixture Phase V in planar geometry. The mode interaction (codimension two) point occurs at a critical value of the frequency of the driving AC voltage. For frequencies below this value the primary pattern-forming instability at the onset voltage is an oblique stationary instability involving oblique rolls, and above this value it is an oscillatory instability giving rise to normal traveling rolls (oriented perpendicular to and traveling in the director direction). The transition has been confirmed by measuring the roll angle and the dominant frequency of the time series, as both quantities exhibit a discontinuous jump across zero when the AC frequency is varied near threshold. The globally coupled system of Ginzburg–Landau equations that qualitatively describe this mode interaction is constructed, and the resulting normal form, in which slow spatial variations of the mode amplitudes are ignored, is analyzed. This analysis shows that the Ginzburg–Landau system provides the adequate theoretical description for the experimentally observed phenomenon. The experimentally observed patterns at and higher above the onset allow us to narrow down the range of the parameters in the normal form. Full article

(This article belongs to the Special Issue Liquid Crystals 2011)

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Open AccessArticle

Interactions of Antibiotics and Methanolic Crude Extracts of Afzelia Africana (Smith.) Against Drug Resistance Bacterial Isolates

by Olayinka Aiyegoro, Adekanmi Adewusi, Sunday Oyedemi, David Akinpelu and Anthony Okoh

Int. J. Mol. Sci. 2011, 12(7), 4477-4487; https://doi.org/10.3390/ijms12074477 - 13 Jul 2011

Cited by 29 | Viewed by 8838

Abstract

Infection due to multidrug resistance pathogens is difficult to manage due to bacterial virulence factors and because of a relatively limited choice of antimicrobial agents. Thus, it is imperative to discover fresh antimicrobials or new practices that are effective for the treatment of [...] Read more.

Infection due to multidrug resistance pathogens is difficult to manage due to bacterial virulence factors and because of a relatively limited choice of antimicrobial agents. Thus, it is imperative to discover fresh antimicrobials or new practices that are effective for the treatment of infectious diseases caused by drug-resistant microorganisms. The objective of this experiment is to investigate for synergistic outcomes when crude methanolic extract of the stem bark of Afzelia africana and antibiotics were combined against a panel of antibiotic resistant bacterial strains that have been implicated in infections. Standard microbiological protocols were used to determine the minimum inhibitory concentrations (MICs) of the extract and antibiotics, as well as to investigate the effect of combinations of the methanolic extract of A. africana stem bark and selected antibiotics using the time-kill assay method. The extract of Afzelia africana exhibited antibacterial activities against both Gram-negative and Gram-positive bacteria made up of environmental and standard strains at a screening concentration of 5 mg/mL. The MICs of the crude extracts and the antibiotics varied between 1 μg/mL and 5.0 mg/mL. Overall, synergistic response constituted about 63.79% of all manner of combinations of extract and antibiotics against all test organisms; antagonism was not detected among the 176 tests carried out. The extract from A. africana stem bark showed potentials of synergy in combination with antibiotics against strains of pathogenic bacteria. The detection of synergy between the extract and antibiotics demonstrates the potential of this plant as a source of antibiotic resistance modulating compounds. Full article

(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming)

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Open AccessReview

Epigenetic Therapy for Breast Cancer

by Feng-Feng Cai, Corina Kohler, Bei Zhang, Ming-Hong Wang, Wei-Jie Chen and Xiao-Yan Zhong

Int. J. Mol. Sci. 2011, 12(7), 4465-4476; https://doi.org/10.3390/ijms12074465 - 11 Jul 2011

Cited by 37 | Viewed by 10160

Abstract

Both genetic and epigenetic alterations can control the progression of cancer. Genetic alterations are impossible to reverse, while epigenetic alterations are reversible. This advantage suggests that epigenetic modifications should be preferred in therapy applications. DNA methyltransferases and histone deacetylases have become the primary [...] Read more.

Both genetic and epigenetic alterations can control the progression of cancer. Genetic alterations are impossible to reverse, while epigenetic alterations are reversible. This advantage suggests that epigenetic modifications should be preferred in therapy applications. DNA methyltransferases and histone deacetylases have become the primary targets for studies in epigenetic therapy. Some DNA methylation inhibitors and histone deacetylation inhibitors are approved by the US Food and Drug Administration as anti-cancer drugs. Therefore, the uses of epigenetic targets are believed to have great potential as a lasting favorable approach in treating breast cancer. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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Open AccessArticle

Silkworm Hemolymph Down-Regulates the Expression of Endoplasmic Reticulum Chaperones under Radiation-Irradiation

by Kyeong Ryong Lee, Seung-Whan Kim, Young Kook Kim, Kisang Kwon, Jong-Soon Choi, Kweon Yu and O-Yu Kwon

Int. J. Mol. Sci. 2011, 12(7), 4456-4464; https://doi.org/10.3390/ijms12074456 - 8 Jul 2011

Cited by 4 | Viewed by 7992

Abstract

We demonstrated that up-regulation of gene expression of endoplasmic reticulum (ER) chaperones (BiP, calnexin, calreticulin, ERp29) and ER membrane kinases (IRE1, PERK, ATF6) was induced by radiation in neuronal PC12 cells. However, addition of silkworm, Bombyx mori, hemolymph to irradiated cells resulted [...] Read more.

We demonstrated that up-regulation of gene expression of endoplasmic reticulum (ER) chaperones (BiP, calnexin, calreticulin, ERp29) and ER membrane kinases (IRE1, PERK, ATF6) was induced by radiation in neuronal PC12 cells. However, addition of silkworm, Bombyx mori, hemolymph to irradiated cells resulted in an obvious decrease in expression of these genes, compared with a single radiation treatment. In contrast, one of the ER chaperones, “ischemia-responsive protein 94 kDa” (irp94), was up-regulated by radiation. However, addition of silkworm hemolymph resulted in no change in the expression of irp94, with an expression pattern that differed from that of ER chaperones. Based on these results, we propose that silkworm hemolymph contains factors that regulate a decrease in the expression of ER chaperones under radiation-irradiation conditions, with the exception of irp94, which is not down-regulated. We suggest that this difference in the molecular character of irp94 may provide a clue to the biological functions associated with ER stress pathways, particularly the effects of radiation. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Klebsiella pneumoniae yggG Gene Product: A Zinc-Dependent Metalloprotease

by Chee Sian Kuan, Mun Teng Wong, Sy Bing Choi, Ching Ching Chang, Yoke Hiang Yee, Habibah A. Wahab, Yahaya Mohd Normi, Wei Cun See Too and Ling Ling Few

Int. J. Mol. Sci. 2011, 12(7), 4441-4455; https://doi.org/10.3390/ijms12074441 - 7 Jul 2011

Cited by 5 | Viewed by 17881

Abstract

Klebsiella pneumoniae causes neonatal sepsis and nosocomial infections. One of the strains, K. pneumoniae MGH 78578, shows high level of resistance to multiple microbial agents. In this study, domain family, amino acid sequence and topology analyses were performed on one of its [...] Read more.

Klebsiella pneumoniae causes neonatal sepsis and nosocomial infections. One of the strains, K. pneumoniae MGH 78578, shows high level of resistance to multiple microbial agents. In this study, domain family, amino acid sequence and topology analyses were performed on one of its hypothetical protein, YggG (KPN_03358). Structural bioinformatics approaches were used to predict the structure and functionality of YggG protein. The open reading frame (ORF) of yggG, which was a putative metalloprotease gene, was also cloned, expressed and characterized. The ORF was PCR amplified from K. pneumoniae MGH 78578 genomic DNA and cloned into a pET14-b vector for heterologous expression in Escherichia coli. The purified YggG protein was subsequently assayed for casein hydrolysis under different conditions. This protein was classified as peptidase M48 family and subclan gluzincin. It was predicted to contain one transmembrane domain by TMpred. Optimal protein expression was achieved by induction with 0.6 mM isopropyl thiogalactoside (IPTG) at 25 °C for six hours. YggG was purified as soluble protein and confirmed to be proteolytically active under the presence of 1.25 mM zinc acetate and showed optimum activity at 37 °C and pH 7.4. We confirmed for the first time that the yggG gene product is a zinc-dependent metalloprotease. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Isolation and Characterization of Microsatellite Loci in the Chinese Cobra Naja atra (Elapidae)

by Long-Hui Lin, Lu-Xi Mao, Xia Luo, Yan-Fu Qu and Xiang Ji

Int. J. Mol. Sci. 2011, 12(7), 4435-4440; https://doi.org/10.3390/ijms12074435 - 7 Jul 2011

Cited by 14 | Viewed by 7159

Abstract

We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong’an and the other in Ganzhou. These markers revealed [...] Read more.

We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong’an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4–12 alleles per locus) and heterozygosity (Ho ranged from 0.213–0.854 and He ranged from 0.301–0.838). Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001) proportion (16.0%) of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low N_m (1.31) value in the two populations from mainland China. Thus, the Yong’an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs). The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra. Full article

(This article belongs to the Section Biochemistry)

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Isoniazid Proliposome Powders for Inhalation—Preparation, Characterization and Cell Culture Studies

by Wipaporn Rojanarat, Narumon Changsan, Ekawat Tawithong, Sirirat Pinsuwan, Hak-Kim Chan and Teerapol Srichana

Int. J. Mol. Sci. 2011, 12(7), 4414-4434; https://doi.org/10.3390/ijms12074414 - 7 Jul 2011

Cited by 103 | Viewed by 11477

Abstract

The aims of this study were to develop proliposome powders containing isoniazid (INH) in a dry powder aerosol form. INH-proliposome powders were prepared by a spray drying method. Proliposome physicochemical properties were determined using cascade impactor, X-ray diffraction and differential scanning calorimetry. The [...] Read more.

The aims of this study were to develop proliposome powders containing isoniazid (INH) in a dry powder aerosol form. INH-proliposome powders were prepared by a spray drying method. Proliposome physicochemical properties were determined using cascade impactor, X-ray diffraction and differential scanning calorimetry. The toxicity of proliposomes to respiratory-associated cell lines and its potential to provoke immunological responses from alveolar macrophages (AM) were determined. Free INH and INH-proliposome bioactivities were tested in vitro and in AM infected with Mycobacterium bovis (M. bovis). Aerosolization properties of INH-proliposome powders at 60 L/min, the powders showed mass median aerodynamic diameters of 2.99–4.92 mm, with fine particle fractions (aerosolized particles less than 4.4 µm) of 15–35%. Encapsulation of INH was 18–30%. Proliposome formulations containing INH to mannitol ratios of 4:6 and 6:4 exhibited the greatest overlapping peak between the drug and mannitol. INH-proliposomes were evidently nontoxic to respiratory-associated cells, and did not activate AM to produce inflammatory mediators—including interleukin-1b (IL-1b), tumor necrosis factor-a (TNF-a), and nitric oxide—at a toxic level. The efficacy of INH-proliposome against AM infected with M. bovis was significantly higher than that of free INH (p < 0.05). INH-proliposomes are potential candidates for an alternative tuberculosis treatment. Full article

(This article belongs to the Section Materials Science)

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Open AccessReview

Enabling Anticancer Therapeutics by Nanoparticle Carriers: The Delivery of Paclitaxel

by Yongjin Liu, Bin Zhang and Bing Yan

Int. J. Mol. Sci. 2011, 12(7), 4395-4413; https://doi.org/10.3390/ijms12074395 - 7 Jul 2011

Cited by 64 | Viewed by 12003

Abstract

Anticancer drugs, such as paclitaxel (PTX), are indispensable for the treatment of a variety of malignancies. However, the application of most drugs is greatly limited by the low water solubility, poor permeability, or high efflux from cells. Nanoparticles have been widely investigated to [...] Read more.

Anticancer drugs, such as paclitaxel (PTX), are indispensable for the treatment of a variety of malignancies. However, the application of most drugs is greatly limited by the low water solubility, poor permeability, or high efflux from cells. Nanoparticles have been widely investigated to enable drug delivery due to their low toxicity, sustained drug release, molecular targeting, and additional therapeutic and imaging functions. This review takes paclitaxel as an example and compares different nanoparticle-based delivery systems for their effectiveness in cancer chemotherapy. Full article

(This article belongs to the Special Issue Bioactive Nanoparticles (special issue))

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Open AccessArticle

Genetic Diversity and Differentiation of the Orange-Spotted Grouper (Epinephelus coioides) Between and Within Cultured Stocks and Wild Populations Inferred from Microsatellite DNA Analysis

by Le Wang, Zining Meng, Xiaochun Liu, Yong Zhang and Haoran Lin

Int. J. Mol. Sci. 2011, 12(7), 4378-4394; https://doi.org/10.3390/ijms12074378 - 6 Jul 2011

Cited by 36 | Viewed by 8714

Abstract

In the present study, we employed microsatellite DNA markers to analyze the genetic diversity and differentiation between and within cultured stocks and wild populations of the orange-spotted grouper originating from the South China Sea and Southeast Asia. Compared to wild populations, genetic changes [...] Read more.

In the present study, we employed microsatellite DNA markers to analyze the genetic diversity and differentiation between and within cultured stocks and wild populations of the orange-spotted grouper originating from the South China Sea and Southeast Asia. Compared to wild populations, genetic changes including reduced genetic diversity and significant differentiation have taken place in cultured grouper stocks, as shown by allele richness and heterozygosity studies, pairwise F_st, structure, molecular variance analysis, as well as multidimensional scaling analysis. Although two geographically adjacent orange-spotted grouper populations in China showed negligible genetic divergence, significant population differentiation was observed in wild grouper populations distributed in a wide geographical area from China, through Malaysia to Indonesia. However, the Mantel test rejected the isolation-by-distance model of genetic structure, which indicated the genetic differentiation among the populations could result from the co-effects of various factors, such as historical dispersal, local environment, ocean currents, river flows and island blocks. Our results demonstrated that microsatellite markers could be suitable not only for genetic monitoring cultured stocks but also for revealing the population structuring of wild orange-spotted grouper populations. Meanwhile, our study provided important information for breeding programs, management of cultured stocks and conservation of wild populations of the orange-spotted grouper. Full article

(This article belongs to the Section Biochemistry)

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Novel Recovery of Nano-Structured Ceria (CeO₂) from Ce(III)-Benzoxazine Dimer Complexes via Thermal Decomposition

by Chatchai Veranitisagul, Attaphon Kaewvilai, Sarawut Sangngern, Worawat Wattanathana, Songwut Suramitr, Nattamon Koonsaeng and Apirat Laobuthee

Int. J. Mol. Sci. 2011, 12(7), 4365-4377; https://doi.org/10.3390/ijms12074365 - 5 Jul 2011

Cited by 32 | Viewed by 9130

Abstract

N,N-bis(2-hydroxybenzyl)alkylamines, benzoxazine dimers, are the major product produced from benzoxazine monomers on mono-functional phenol by the one step ring opening reaction. Due to the metal responsive property of benzoxazine dimers, in this present work, N,N-bis(5-methyl-2-hydroxybenzyl)methylamine (MMD), N,N [...] Read more.

N,N-bis(2-hydroxybenzyl)alkylamines, benzoxazine dimers, are the major product produced from benzoxazine monomers on mono-functional phenol by the one step ring opening reaction. Due to the metal responsive property of benzoxazine dimers, in this present work, N,N-bis(5-methyl-2-hydroxybenzyl)methylamine (MMD), N,N-bis (5-ethyl-2-hydroxybenzyl)methylamine (EMD), and N,N-bis(5-methoxy-2-hydroxybenzyl) methyl amine (MeMD), are considered as novel ligands for rare earth metal ion, such as cerium(III) ion. The complex formed when the clear and colorless solutions of cerium nitrate and benzoxazine dimers were mixed, results in a brown colored solution. The metal-ligand ratios determined by the molar ratio and the Job’s methods were found to be in a ratio of 1:6. To clarify the evidence of the complex formation mechanism, the interactions among protons in benzoxazine dimers both prior to and after the formation of complexes were determined by means of ¹H-NMR, 2D-NMR and a computational simulation. The single phase ceria (CeO₂) was successfully prepared by thermal decomposition of the Ce(III)-benzoxazine dimer complexes at 600 °C for 2 h, was then characterized using XRD. In addition, the ceria powder investigated by TEM is spherical with an average diameter of 20 nm. Full article

(This article belongs to the Section Materials Science)

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Predictivity Approach for Quantitative Structure-Property Models. Application for Blood-Brain Barrier Permeation of Diverse Drug-Like Compounds

by Sorana D. Bolboacă and Lorentz Jäntschi

Int. J. Mol. Sci. 2011, 12(7), 4348-4364; https://doi.org/10.3390/ijms12074348 - 5 Jul 2011

Cited by 17 | Viewed by 7745

Abstract

The goal of the present research was to present a predictivity statistical approach applied on structure-based prediction models. The approach was applied to the domain of blood-brain barrier (BBB) permeation of diverse drug-like compounds. For this purpose, 15 statistical parameters and associated 95% [...] Read more.

The goal of the present research was to present a predictivity statistical approach applied on structure-based prediction models. The approach was applied to the domain of blood-brain barrier (BBB) permeation of diverse drug-like compounds. For this purpose, 15 statistical parameters and associated 95% confidence intervals computed on a 2 × 2 contingency table were defined as measures of predictivity for binary quantitative structure-property models. The predictivity approach was applied on a set of compounds comprised of 437 diverse molecules, 122 with measured BBB permeability and 315 classified as active or inactive. A training set of 81 compounds (~2/3 of 122 compounds assigned randomly) was used to identify the model and a test set of 41 compounds was used as the internal validation set. The molecular descriptor family on vertices cutting was the computation tool used to generate and calculate structural descriptors for all compounds. The identified model was assessed using the predictivity approach and compared to one model previously reported. The best-identified classification model proved to have an accuracy of 69% in the training set (95%CI [58.53–78.37]) and of 73% in the test set (95%CI [58.32–84.77]). The predictive accuracy obtained on the external set proved to be of 73% (95%CI [67.58–77.39]). The classification model proved to have better abilities in the classification of inactive compounds (specificity of ~74% [59.20–85.15]) compared to abilities in the classification of active compounds (sensitivity of ~64% [48.47–77.70]) in the training and external sets. The overall accuracy of the previously reported model seems not to be statistically significantly better compared to the identified model (~81% [71.45–87.80] in the training set, ~93% [78.12–98.17] in the test set and ~79% [70.19–86.58] in the external set). In conclusion, our predictivity approach allowed us to characterize the model obtained on the investigated set of compounds as well as compare it with a previously reported model. According to the obtained results, the reported model should be chosen if a correct classification of inactive compounds is desired and the previously reported model should be chosen if a correct classification of active compounds is most wanted. Full article

(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)

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Open AccessReview

To Remove or Not to Remove? The Challenge of Extracting the Template to Make the Cavities Available in Molecularly Imprinted Polymers (MIPs)

by Rosa A. Lorenzo, Antonia M. Carro, Carmen Alvarez-Lorenzo and Angel Concheiro

Int. J. Mol. Sci. 2011, 12(7), 4327-4347; https://doi.org/10.3390/ijms12074327 - 5 Jul 2011

Cited by 159 | Viewed by 16535

Abstract

Template removal is a critical step in the preparation of most molecularly imprinted polymers (MIPs). The polymer network itself and the affinity of the imprinted cavities for the template make its removal hard. If there are remaining template molecules in the MIPs, less [...] Read more.

Template removal is a critical step in the preparation of most molecularly imprinted polymers (MIPs). The polymer network itself and the affinity of the imprinted cavities for the template make its removal hard. If there are remaining template molecules in the MIPs, less cavities will be available for rebinding, which decreases efficiency. Furthermore, if template bleeding occurs during analytical applications, errors will arise. Despite the relevance to the MIPs performance, template removal has received scarce attention and is currently the least cost-effective step of the MIP development. Attempts to reach complete template removal may involve the use of too drastic conditions in conventional extraction techniques, resulting in the damage or the collapse of the imprinted cavities. Advances in the extraction techniques in the last decade may provide optimized tools. The aim of this review is to analyze the available data on the efficiency of diverse extraction techniques for template removal, paying attention not only to the removal yield but also to MIPs performance. Such an analysis is expected to be useful for opening a way to rational approaches for template removal (minimizing the costs of solvents and time) instead of the current trial-and-error methods. Full article

(This article belongs to the Special Issue Molecular Imprinting Science and Technology)

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Molecular Characterization of Tob1 in Muscle Development in Pigs

by Jing Yuan, Ji-Yue Cao, Zhong-Lin Tang, Ning Wang and Kui Li

Int. J. Mol. Sci. 2011, 12(7), 4315-4326; https://doi.org/10.3390/ijms12074315 - 4 Jul 2011

Cited by 9 | Viewed by 7442

Abstract

Cell proliferation is an important biological process during myogenesis. Tob1 encoded a member of the Tob/BTG family of anti-proliferative proteins. Our previous LongSAGE (Long Serial Analysis of Gene Expression) analysis suggested that Tob1 was differentially expressed during prenatal skeletal muscle development. In this [...] Read more.

Cell proliferation is an important biological process during myogenesis. Tob1 encoded a member of the Tob/BTG family of anti-proliferative proteins. Our previous LongSAGE (Long Serial Analysis of Gene Expression) analysis suggested that Tob1 was differentially expressed during prenatal skeletal muscle development. In this study, we isolated and characterized the swine Tob1 gene. Subsequently, we examined Tob1 chromosome assignment, subcellular localization and dynamic expression profile in prenatal skeletal muscle (33, 65 and 90 days post-conception, dpc) from Landrace (lean-type) and Tongcheng pigs (obese-type). The Tob1 gene was mapped to pig chromosome 12 (SSC12). The Tob1 protein was distributed throughout the nucleus and cytoplasm of PK15 cells. During prenatal skeletal muscle development, Tob1 was up-regulated and highly expressed in skeletal muscle at 90 dpc in Tongcheng pigs but peaked at 65 dpc in Landrace pigs. This result suggested that there were different proliferation patterns during myogenesis between Tongcheng and Landrace pigs. During postnatal skeletal muscle development, the expression of Tob1 increased with aging, indicating that the proliferation potential of myoblasts decreased in postnatal muscle development. In tissues of adult wuzhishan miniature pigs, the Tob1 gene was highly expressed in skeletal muscle. The expression of Tob1 was significantly increased at day 6 during C2C12 differentiation time, suggesting a possible role in skeletal muscle development. Therefore, this study indicated that Tob1 perhaps played an important role in skeletal muscle development. Full article

(This article belongs to the Section Biochemistry)

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Int. J. Mol. Sci., Volume 12, Issue 7 (July 2011) – 39 articles , Pages 4180-4757

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