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Open AccessReview Recent Advances in Conotoxin Classification by Using Machine Learning Methods
Molecules 2017, 22(7), 1057; doi:10.3390/molecules22071057
Received: 17 May 2017 / Revised: 12 June 2017 / Accepted: 19 June 2017 / Published: 25 June 2017
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Abstract
Conotoxins are disulfide-rich small peptides, which are invaluable peptides that target ion channel and neuronal receptors. Conotoxins have been demonstrated as potent pharmaceuticals in the treatment of a series of diseases, such as Alzheimer’s disease, Parkinson’s disease, and epilepsy. In addition, conotoxins are
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Conotoxins are disulfide-rich small peptides, which are invaluable peptides that target ion channel and neuronal receptors. Conotoxins have been demonstrated as potent pharmaceuticals in the treatment of a series of diseases, such as Alzheimer’s disease, Parkinson’s disease, and epilepsy. In addition, conotoxins are also ideal molecular templates for the development of new drug lead compounds and play important roles in neurobiological research as well. Thus, the accurate identification of conotoxin types will provide key clues for the biological research and clinical medicine. Generally, conotoxin types are confirmed when their sequence, structure, and function are experimentally validated. However, it is time-consuming and costly to acquire the structure and function information by using biochemical experiments. Therefore, it is important to develop computational tools for efficiently and effectively recognizing conotoxin types based on sequence information. In this work, we reviewed the current progress in computational identification of conotoxins in the following aspects: (i) construction of benchmark dataset; (ii) strategies for extracting sequence features; (iii) feature selection techniques; (iv) machine learning methods for classifying conotoxins; (v) the results obtained by these methods and the published tools; and (vi) future perspectives on conotoxin classification. The paper provides the basis for in-depth study of conotoxins and drug therapy research. Full article
(This article belongs to the Special Issue Computational Analysis for Protein Structure and Interaction)
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Open AccessArticle Control of Corner Separation with Plasma Actuation in a High-Speed Compressor Cascade
Appl. Sci. 2017, 7(5), 465; doi:10.3390/app7050465
Received: 31 March 2017 / Revised: 25 April 2017 / Accepted: 25 April 2017 / Published: 29 April 2017
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Abstract
The performances of modern highly loaded compressors are limited by the corner separations. Plasma actuation is a typical active flow control methodology, which has been proven to be capable of controlling the corner separations in low-speed compressor cascades. The main purpose of this
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The performances of modern highly loaded compressors are limited by the corner separations. Plasma actuation is a typical active flow control methodology, which has been proven to be capable of controlling the corner separations in low-speed compressor cascades. The main purpose of this paper is to uncover the flow control law and the mechanism of high-speed compressor cascade corner separation control with plasma actuations. The control effects of the suction surface as well as the endwall plasma actuations in suppressing the high-speed compressor cascade flow separations are investigated with numerical methods. The main flow structures within the high-speed compressor cascade corner separation and the development of the corresponding flow loss are investigated firstly. Next, the performances of plasma actuations in suppressing the high-speed compressor cascade corner separation are studied. At last, the mechanisms behind the control effects of the suction surface and the endwall plasma actuations are discussed. Both the suction surface and the endwall plasma actuations can improve the high-speed compressor cascade static pressure rise coefficient, while reducing the corresponding total pressure loss and blockage coefficients. The suction surface plasma actuation can suppress not only the high-speed compressor cascade corner separation vortex but also the airfoil separation, so, compared to the endwall plasma actuation, the suction surface plasma actuation is more efficient in reducing the total pressure loss of the high-speed compressor cascade. However, through suppressing the development of the passage vortex, the endwall plasma actuation is more efficient in reducing the flow blockage and improving the static pressure rise of the high-speed compressor cascade. Full article
(This article belongs to the Special Issue Active Flow Control Technologies for Energy and Propulsive Systems)
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Open AccessArticle New Potential Biomarker for Methasterone Misuse in Human Urine by Liquid Chromatography Quadrupole Time of Flight Mass Spectrometry
Int. J. Mol. Sci. 2016, 17(10), 1628; doi:10.3390/ijms17101628
Received: 11 July 2016 / Revised: 14 September 2016 / Accepted: 19 September 2016 / Published: 24 September 2016
Cited by 1 | Viewed by 599 | PDF Full-text (2162 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In this study, methasterone urinary metabolic profiles were investigated by liquid chromatography quadrupole time of flight mass spectrometry (LC-QTOF-MS) in full scan and targeted MS/MS modes with accurate mass measurement. A healthy male volunteer was asked to take the drug and liquid–liquid extraction
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In this study, methasterone urinary metabolic profiles were investigated by liquid chromatography quadrupole time of flight mass spectrometry (LC-QTOF-MS) in full scan and targeted MS/MS modes with accurate mass measurement. A healthy male volunteer was asked to take the drug and liquid–liquid extraction was employed to process urine samples. Chromatographic peaks for potential metabolites were hunted out with the theoretical [M − H] as a target ion in a full scan experiment and actual deprotonated ions were studied in targeted MS/MS experiment. Fifteen metabolites including two new sulfates (S1 and S2), three glucuronide conjugates (G2, G6 and G7), and three free metabolites (M2, M4 and M6) were detected for methasterone. Three metabolites involving G4, G5 and M5 were obtained for the first time in human urine samples. Owing to the absence of helpful fragments to elucidate the steroid ring structure of methasterone phase II metabolites, gas chromatography mass spectrometry (GC-MS) was employed to obtain structural information of the trimethylsilylated phase I metabolite released after enzymatic hydrolysis and the potential structure was inferred using a combined MS method. Metabolite detection times were also analyzed and G2 (18-nor-17β-hydroxymethyl-2α, 17α-dimethyl-androst-13-en-3α-ol-ξ-O-glucuronide) was thought to be new potential biomarker for methasterone misuse which can be detected up to 10 days. Full article
(This article belongs to the Special Issue Metabolomic Technologies in Medicine)
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Open AccessArticle Synthesis and Biological Evaluation of RGD-Conjugated MEK1/2 Kinase Inhibitors for Integrin-Targeted Cancer Therapy
Molecules 2013, 18(11), 13957-13978; doi:10.3390/molecules181113957
Received: 27 September 2013 / Revised: 12 October 2013 / Accepted: 15 October 2013 / Published: 12 November 2013
Cited by 6 | Viewed by 2158 | PDF Full-text (863 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Two novel series of RGD-MEKI conjugates derived from a MEK1/2 kinase inhibitor—PD0325901—have been developed for integrin receptor mediated anticancer therapy. The first series, alkoxylamine analog RGD-MEKI conjugates 9ag showed anti-proliferation activity in melanoma A375 cells by the same mechanism as that
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Two novel series of RGD-MEKI conjugates derived from a MEK1/2 kinase inhibitor—PD0325901—have been developed for integrin receptor mediated anticancer therapy. The first series, alkoxylamine analog RGD-MEKI conjugates 9ag showed anti-proliferation activity in melanoma A375 cells by the same mechanism as that of PD0325901. PEGylation increased the IC50 value of 9f three-fold in the A375 assay, and the multi-cRGD peptide cargo significantly improved the receptor specific anti-proliferation activity of 9g in integrin-overexpressing U87 cells. In the second series, RGD-PD0325901 13 exhibited significantly increased antitumor properties compared to the alkoxylamine analogs by both inhibition of the ERK pathway activity and DNA replication of the cancer cells. Furthermore, 13 displayed more potent anti-proliferation activity in the U87 assay than PD0325901 in a dose-dependent manner. All these data demonstrate that RGD-MEKI conjugates with an ester bond linkage enhanced anticancer efficacy with improved targeting capability toward integrin-overexpressing tumor cells. Full article
(This article belongs to the Section Medicinal Chemistry)
Open AccessArticle Substituted 3-Benzylcoumarins as Allosteric MEK1 Inhibitors: Design, Synthesis and Biological Evaluation as Antiviral Agents
Molecules 2013, 18(5), 6057-6091; doi:10.3390/molecules18056057
Received: 25 April 2013 / Revised: 10 May 2013 / Accepted: 14 May 2013 / Published: 21 May 2013
Cited by 6 | Viewed by 2231 | PDF Full-text (1413 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In order to find novel antiviral agents, a series of allosteric MEK1 inhibitors were designed and synthesized. Based on docking results, multiple optimizations were made on the coumarin scaffold. Some of the derivatives showed excellent MEK1 binding affinity in the appropriate enzymatic assays
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In order to find novel antiviral agents, a series of allosteric MEK1 inhibitors were designed and synthesized. Based on docking results, multiple optimizations were made on the coumarin scaffold. Some of the derivatives showed excellent MEK1 binding affinity in the appropriate enzymatic assays and displayed obvious inhibitory effects on the ERK pathway in a cellular assay. These compounds also significantly inhibited virus (EV71) replication in HEK293 and RD cells. Several compounds showed potential as agents for the treatment of viral infective diseases, with the most potent compound 18 showing an IC50 value of 54.57 nM in the MEK1 binding assay. Full article
(This article belongs to the Section Medicinal Chemistry)
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