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https://www.readbyqxmd.com/read/28813000/an-ameliorated-prediction-of-drug-target-interactions-based-on-multi-scale-discrete-wavelet-transform-and-network-features
#1
Cong Shen, Yijie Ding, Jijun Tang, Xinying Xu, Fei Guo
The prediction of drug-target interactions (DTIs) via computational technology plays a crucial role in reducing the experimental cost. A variety of state-of-the-art methods have been proposed to improve the accuracy of DTI predictions. In this paper, we propose a kind of drug-target interactions predictor adopting multi-scale discrete wavelet transform and network features (named as DAWN) in order to solve the DTIs prediction problem. We encode the drug molecule by a substructure fingerprint with a dictionary of substructure patterns...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812260/zinc-metabolism-and-metallothioneins
#2
REVIEW
Abdulkerim Kasim Baltaci, Kemal Yuce, Rasim Mogulkoc
Among the trace elements, zinc is one of the most used elements in biological systems. Zinc is found in the structure of more than 2700 enzymes, including hydrolases, transferases, oxyreductases, ligases, isomerases, and lyases. Not surprisingly, it is present in almost all body cells. Preserving the stability and integrity of biological membranes and ion channels, zinc is also an intracellular regulator and provides structural support to proteins during molecular interactions. It acts as a structural element in nucleic acids or other gene-regulating proteins...
August 15, 2017: Biological Trace Element Research
https://www.readbyqxmd.com/read/28811463/a-light-regulated-host-guest-based-nanochannel-system-inspired-by-channelrhodopsins-protein
#3
Yue Sun, Junkai Ma, Fan Zhang, Fei Zhu, Yuxiao Mei, Lu Liu, Demei Tian, Haibing Li
The light-controlled gating of ion transport across membranes is central to nature (e.g., in protein channels). Herein, inspired by channelrhodopsins, we introduce a facile non-covalent approach towards light-responsive biomimetic channelrhodopsin nanochannels using host-guest interactions between a negative pillararene host and a positive azobenzene guest. By switching between threading and dethreading states with alternating visible and UV light irradiation, the functional channels can be flexible to regulate the inner surface charge of the channels, which in turn was exploited to achieve different forms of ion transport, for instance, cation-selective transport and anion-selective transport...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811018/direct-coupling-of-electromembrane-extraction-to-mass-spectrometry-advancing-the-probe-functionality-toward-measurements-of-zwitterionic-drug-metabolites
#4
Torstein Kige Rye, David Fuchs, Stig Pedersen-Bjergaard, Nickolaj Jacob Petersen
A triple-flow electromembrane extraction (EME) probe was developed and coupled directly to electrospray-ionization mass spectrometry (ESI-MS). Metabolic reaction mixtures (pH 7.4) containing drug substances and related metabolites were continuously drawn (20 μL/min) into the EME probe in one flow channel, and mixed inside the probe with 7.5 μL min(-1) of 1 M formic acid as make-up flow from a second flow channel. Following this acidification, the drug substances and their related metabolites were continuously extracted by EME at 400 V, across a supported liquid membrane (SLM) comprising 2-nitrophenyl octyl ether (and for some experiments containing 30% triphenyl phosphate (TPP)), and into 20 μL min(-1) of formic acid as acceptor phase, which was introduced through a third flow channel...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28810916/the-catsper-channel-and-its-roles-in-male-fertility-a-systematic-review
#5
REVIEW
Xiang-Hong Sun, Ying-Ying Zhu, Lin Wang, Hong-Ling Liu, Yong Ling, Zong-Li Li, Li-Bo Sun
The Catsper channel is a sperm-specific, Ca(2+)-permeable, pH-dependent, and low voltage-dependent channel that is essential for the hyperactivity of sperm flagellum, chemotaxis towards the egg, capacitation and acrosome reaction. All of these physiological events require calcium entry into sperm cells. Remarkably, Catsper genes are exclusively expressed in the testis during spermatogenesis, and are sensitive to ion channel-induced pH change, such as NHEs, Ca(2+)ATPase, K(+) channel, Hv1 channel and HCO3(-) transporters...
August 15, 2017: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/28810912/inhibition-of-trpm7-suppresses-cell-proliferation-of-colon-adenocarcinoma-in-vitro-and-induces-hypomagnesemia-in-vivo-without-affecting-azoxymethane-induced-early-colon-cancer-in-mice
#6
Junhao Huang, Hideki Furuya, Malika Faouzi, Zheng Zhang, Mahealani Monteilh-Zoller, F Kelly Galbraith Kawabata, David Horgen, Toshihiko Kawamori, Reinhold Penner, Andrea Fleig
BACKGROUND: Magnesium (Mg(2+)) is an essential cation implicated in carcinogenesis, solid tumor progression and metastatic potential. The Transient Receptor Potential Melastatin Member 7 (TRPM7) is a divalent ion channel involved in cellular and systemic Mg(2+) homeostasis. Abnormal expression of TRPM7 is found in numerous cancers, including colon, implicating TRPM7 in this process. METHODS: To establish a possible link between systemic magnesium (Mg(2+)) status, the Mg(2+) conducting channel TRPM7 in colon epithelial cells, and colon carcinogenesis, in vitro whole-cell patch clamp electrophysiology, qPCR, and pharmacological tools were used probing human colorectal adenocarcinoma HT-29 as well as normal primary mouse colon epithelial cells...
August 15, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/28810874/sudden-cardiac-death-focus-on-the-genetics-of-channelopathies-and-cardiomyopathies
#7
REVIEW
Simona Magi, Vincenzo Lariccia, Marta Maiolino, Salvatore Amoroso, Santo Gratteri
Sudden cardiac death (SCD) describes a natural and unexpected death from cardiac causes occurring within a short period of time (generally within 1 h of symptom onset) in the absence of any other potentially lethal condition. Most SCD-related diseases have a genetic basis; in particular congenital cardiac channelopathies and cardiomyopathies have been described as leading causes of SCD. Congenital cardiac channelopathies are primary electric disorders caused by mutations affecting genes encoding cardiac ion channels or associated proteins, whereas cardiomyopathies are related to mutations in genes encoding several categories of proteins, including those of sarcomeres, desmosomes, the cytoskeleton, and the nuclear envelope...
August 15, 2017: Journal of Biomedical Science
https://www.readbyqxmd.com/read/28810709/parallel-evolution-of-sperm-hyper-activation-ca2-channels
#8
Jacob C Cooper, Nitin Phadnis
Sperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+ into the sperm flagellum via CatSper ion channels. Surprisingly, all nine CatSper genes have been independently lost in several animal lineages. In Drosophila, sperm hyper-activation is performed through the cooption of the polycystic kidney disease 2 (pkd2) Ca2+ channel. The parallels between CatSpers in primates and pkd2 in Drosophila provide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by > 500 million years of divergence...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28809766/crispr-cas9-editing-of-nf1-gene-identifies-crmp2-as-a-therapeutic-target-in-neurofibromatosis-type-1-related-pain-that-is-reversed-by-s-lacosamide
#9
Aubin Moutal, Xiaofang Yang, Wennan Li, Kerry B Gilbraith, Shizhen Luo, Song Cai, Liberty François-Moutal, Lindsey A Chew, Seul Ki Yeon, Shreya S Bellampalli, Chaoling Qu, Jennifer Y Xie, Mohab M Ibrahim, May Khanna, Ki Duk Park, Frank Porreca, Rajesh Khanna
Neurofibromatosis type 1 (NF1) is a rare autosomal dominant disease linked to mutations of the Nf1 gene. Patients with NF1 commonly experience severe pain. Studies on mice with Nf1 haploinsufficiency have been instructive in identifying sensitization of ion channels as a possible cause underlying the heightened pain suffered by patients with NF1. However, behavioral assessments of Nf1 mice have led to uncertain conclusions about the potential causal role of Nf1 in pain. We used the clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (CRISPR/Cas9) genome editing system to create and mechanistically characterize a novel rat model of NF1-related pain...
July 3, 2017: Pain
https://www.readbyqxmd.com/read/28809765/cyclin-dependent-kinase-5-modulates-the-p2x2a-receptor-channel-gating-through-phosphorylation-of-c-terminal-threonine-372
#10
Claudio Coddou, Rodrigo Sandoval, Patricio Castro, Pablo Lazcano, Maria José Hevia, Milos Rokic, Bradford Hall, Anita Terse, Christian Gonzalez-Billault, Ashok B Kulkarni, Stanko S Stojilkovic, Elias Utreras
The purinergic P2X2 receptor (P2X2R) is an adenosine triphosphate-gated ion channel widely expressed in the nervous system. Here, we identified a putative cyclin-dependent kinase 5 (Cdk5) phosphorylation site in the full-size variant P2X2aR (TPKH), which is absent in the splice variant P2X2bR. We therefore investigated the effects of Cdk5 and its neuronal activator, p35, on P2X2aR function. We found an interaction between P2X2aR and Cdk5/p35 by co-immunofluorescence and co-immunoprecipitation in HEK293 cells...
July 17, 2017: Pain
https://www.readbyqxmd.com/read/28809537/confined-water-structure-dynamics-and-thermodynamics
#11
Sudip Chakraborty, Hemant Kumar, Chandan Dasgupta, Prabal K Maiti
Understanding the properties of strongly confined water is important for a variety of applications such as fast flow and desalination devices, voltage generation, flow sensing, and nanofluidics. Confined water also plays an important role in many biological processes such as flow through ion channels. Water in the bulk exhibits many unusual properties that arise primarily from the presence of a network of hydrogen bonds. Strong confinement in structures such as carbon nanotubes (CNTs) substantially modifies the structural, thermodynamic, and dynamic (both translational and orientational) properties of water by changing the structure of the hydrogen bond network...
August 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28809075/allosteric-modulation-of-%C3%AE-4%C3%AE-2-nicotinic-acetylcholine-receptors-desformylflustrabromine-potentiates-antiallodynic-response-of-nicotine-in-a-mouse-model-of-neuropathic-pain
#12
D Bagdas, D Ergun, A Jackson, W Toma, M K Schulte, M I Damaj
BACKGROUND: Neuronal nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels. The α4β2 subtype of nAChRs plays an important role in the mediation of pain and several nicotine-evoked responses. Agonists and partial agonists of α4β2 nAChRs show efficacy in animal pain models. In addition, the antinociceptive properties of nicotine, a non-selective nAChR agonist with a high affinity for α4β2 nAChRs, is well-known. There is a growing body of evidence pointing to allosteric modulation of nAChRs as an alternative treatment strategy in experimental pain...
August 14, 2017: European Journal of Pain: EJP
https://www.readbyqxmd.com/read/28808992/a-photoaffinity-labeling-based-chemoproteomics-strategy-for-unbiased-target-deconvolution-of-small-molecule-drug-candidates
#13
Jason R Thomas, Scott M Brittain, Jennifer Lipps, Luis Llamas, Rishi K Jain, Markus Schirle
The combination of photoaffinity labeling (PAL) and quantitative chemoproteomics enables the comprehensive, unbiased determination of protein interaction profiles to support target identification of bioactive small molecules. This approach is amenable to cells in culture and compatible with pharmacologically relevant transmembrane target classes like G-protein coupled receptors and ions channels which have been notoriously hard to access by conventional chemoproteomics approaches. Here, we describe a strategy that combines PAL probe titration and competition with excess parental compounds with the goal of enabling the identification of specific interactors as well as assessing the functional relevance of a binding event for the phenotype under investigation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808275/screening-drug-target-interactions-with-positive-unlabeled-learning
#14
Lihong Peng, Wen Zhu, Bo Liao, Yu Duan, Min Chen, Yi Chen, Jialiang Yang
Identifying drug-target interaction (DTI) candidates is crucial for drug repositioning. However, usually only positive DTIs are deposited in known databases, which challenges computational methods to predict novel DTIs due to the lack of negative samples. To overcome this dilemma, researchers usually randomly select negative samples from unlabeled drug-target pairs, which introduces a lot of false-positives. In this study, a negative sample extraction method named NDTISE is first developed to screen strong negative DTI examples based on positive-unlabeled learning...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808008/mathematical-model-reveals-role-of-nucleotide-signaling-in-airway-surface-liquid-homeostasis-and-its-dysregulation-in-cystic-fibrosis
#15
Conner I Sandefur, Richard C Boucher, Timothy C Elston
Mucociliary clearance is composed of three components (i.e., mucin secretion, airway surface hydration, and ciliary-activity) which function coordinately to clear inhaled microbes and other foreign particles from airway surfaces. Airway surface hydration is maintained by water fluxes driven predominantly by active chloride and sodium ion transport. The ion channels that mediate electrogenic ion transport are regulated by extracellular purinergic signals that signal through G protein-coupled receptors. These purinoreceptors and the signaling pathways they activate have been identified as possible therapeutic targets for treating lung disease...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807147/trpp2-ion-channels-critical-regulators-of-organ-morphogenesis-in-health-and-disease
#16
REVIEW
Tilman Busch, Michael Köttgen, Alexis Hofherr
Ion channels control the membrane potential and mediate transport of ions across membranes. Archetypical physiological functions of ion channels include processes such as regulation of neuronal excitability, muscle contraction, or transepithelial ion transport. In that regard, transient receptor potential ion channel polycystin 2 (TRPP2) is remarkable, because it controls complex morphogenetic processes such as the establishment of properly shaped epithelial tubules and left-right-asymmetry of organs. The fascinating question of how an ion channel regulates morphogenesis has since captivated the attention of scientists in different disciplines...
September 2017: Cell Calcium
https://www.readbyqxmd.com/read/28807146/trp-channel-pores-and-local-calcium-signals
#17
REVIEW
Marie Mulier, Joris Vriens, Thomas Voets
Calcium signals control a plethora of essential cellular functions ranging from secretion and contraction to gene expression and sensory signaling cascades. An essential part of intracellular calcium signals originates from the transmembrane flux of calcium ions, which is mainly mediated through different calcium-permeable cation channels with variable calcium selectivity. Opening of individual calcium permeable channels induces a local cytosolic calcium rise that can be highly restricted in time and space...
September 2017: Cell Calcium
https://www.readbyqxmd.com/read/28807145/a-benzothiadiazine-derivative-and-methylprednisolone-are-novel-and-selective-activators-of-transient-receptor-potential-canonical-5-trpc5-channels
#18
Holger Beckmann, Julia Richter, Kerstin Hill, Nicole Urban, Horst Lemoine, Michael Schaefer
The transient receptor potential canonical channel 5 (TRPC5) is a Ca(2+)-permeable ion channel, which is predominantly expressed in the brain. TRPC5-deficient mice exhibit a reduced innate fear response and impaired motor control. In addition, outgrowth of hippocampal and cerebellar neurons is retarded by TRPC5. However, pharmacological evidence of TRPC5 function on cellular or organismic levels is sparse. Thus, there is still a need for identifying novel and efficient TRPC5 channel modulators. We, therefore, screened compound libraries and identified the glucocorticoid methylprednisolone and N-[3-(adamantan-2-yloxy)propyl]-3-(6-methyl-1,1-dioxo-2H-1λ(6),2,4-benzothiadiazin-3-yl)propanamide (BTD) as novel TRPC5 activators...
September 2017: Cell Calcium
https://www.readbyqxmd.com/read/28807144/regulation-of-l-type-cav1-3-channel-activity-and-insulin-secretion-by-the-cgmp-pkg-signaling-pathway
#19
Alejandro Sandoval, Paz Duran, María A Gandini, Arturo Andrade, Angélica Almanza, Simon Kaja, Ricardo Felix
cGMP is a second messenger widely used in the nervous system and other tissues. One of the major effectors for cGMP is the serine/threonine protein kinase, cGMP-dependent protein kinase (PKG), which catalyzes the phosphorylation of a variety of proteins including ion channels. Previously, it has been shown that the cGMP-PKG signaling pathway inhibits Ca(2+) currents in rat vestibular hair cells and chromaffin cells. This current allegedly flow through voltage-gated CaV1.3L-type Ca(2+) channels, and is important for controlling vestibular hair cell sensory function and catecholamine secretion, respectively...
September 2017: Cell Calcium
https://www.readbyqxmd.com/read/28807015/genomic-upregulation-of-cardiac-cav1-2%C3%AE-and-ncx1-by-estrogen-in-women
#20
Rita Papp, Glenna C L Bett, Agnieszka Lis, Randall L Rasmusson, István Baczkó, András Varró, Guy Salama
BACKGROUND: Women have a higher risk of lethal arrhythmias than men in long QT syndrome type 2 (LQTS2), but the mechanisms remain uncertain due to the limited availability of healthy control human tissue. We have previously reported that in female rabbits, estrogen increases arrhythmia risk in drug-induced LQTS2 by upregulating L-type Ca(2+) (ICa,L) and sodium-calcium exchange (INCX) currents at the base of the epicardium by a genomic mechanism. This study investigates if the effects of estrogen on rabbit ICa,L and INCX apply to human hearts...
August 14, 2017: Biology of Sex Differences
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