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https://www.readbyqxmd.com/read/28107751/molecular-modeling-study-of-cp-690550-derivatives-as-jak3-kinase-inhibitors-through-combined-3d-qsar-molecular-docking-and-dynamics-simulation-techniques
#1
Jing Li Wang, Li Ping Cheng, Tian Chi Wang, Wei Deng, Fan Hong Wu
To develop more potent JAK3 kinase inhibitors, a series of CP-690550 derivatives were investigated using combined molecular modeling techniques, such as 3D-QSAR, molecular docking and molecular dynamics (MD). The leave-one-out correlation (q(2)) and non-cross-validated correlation coefficient (r(2)) of the best CoMFA model are 0.715 and 0.992, respectively. The q(2) and r(2) values of the best CoMSIA model are 0.739 and 0.995, respectively. The steric, electrostatic, and hydrophobic fields played important roles in determining the inhibitory activity of CP-690550 derivatives...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28107695/antibacterial-activity-computational-analysis-and-host-toxicity-study-of-thymol-sulfonamide-conjugates
#2
Shasank S Swain, Sudhir K Paidesetty, Rabindra N Padhy
Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus faecalis (VRE) are notorious pathogenic multidrug resistant (MDR) bacteria in both hospital and community sectors, and today the first antibacterial drug sulfamethoxazole is ineffective. The monoterpene phenol, thymol was conjugated with seven sulfa drug derivatives individually, adopting the dye-azo synthesis protocol, and conjugates were characterized using spectral analysis techniques such as, UV, FTIR, MS, HPLC, (1)H NMR, (13)C NMR and SEM...
January 17, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28107503/osteopontin-affects-insulin-vesicle-localization-and-ca2-homeostasis-in-pancreatic-beta-cells-from-female-mice
#3
Anna Wendt, Inês G Mollet, Anki Knutsson, Victor S Bolmgren, Anna Hultgårdh-Nilsson, Maria F Gomez, Lena Eliasson
Type 2 diabetic patients suffer from insulin resistance and reduced insulin secretion. Osteopontin (OPN), a versatile protein expressed in several tissues throughout the body including the islets of Langerhans, has previously been implicated in the development of insulin resistance. Here we have investigated the role of OPN in insulin secretion using an OPN knock out mouse model (OPN-/-). Ultra-structural analyzes of islets from OPN-/- and WT mice indicated weaker cell-cell connections between the islet cells in the OPN-/- mouse compared to WT...
2017: PloS One
https://www.readbyqxmd.com/read/28107379/experimental-and-in-silico-investigation-of-anti-microbial-activity-of-1-chloro-2-isocyanatoethane-derivatives-of-thiomorpholine-piperazine-and-morpholine
#4
Charles O Nwuche, Oguejiofo T Ujam, Akachukwu Ibezim, Ifeoma B Ujam
The Antibiogram properties of 1-chloro-2-isocyanatoethane derivatives of thiomorpholine (CTC), piperazine (CPC) and morpholine (CMC) were evaluated by the approved agar well diffusion, the minimum inhibitory concentration (MIC) and in silico techniques. A total of fourteen microbial cultures consisting of ten bacteria and four yeast strains were used in the biological study while affinity of the compounds for DNA gyrase, a validated antibacterial drug target, was investigated by docking method. Results indicate that both thiomorpholine and piperazine had zero activity against the Gram negative organisms tested...
2017: PloS One
https://www.readbyqxmd.com/read/28106755/the-performance-of-several-docking-programs-at-reproducing-protein-macrolide-like-crystal-structures
#5
Alejandro Castro-Alvarez, Anna M Costa, Jaume Vilarrasa
The accuracy of five docking programs at reproducing crystallographic structures of complexes of 8 macrolides and 12 related macrocyclic structures, all with their corresponding receptors, was evaluated. Self-docking calculations indicated excellent performance in all cases (mean RMSD values ≤ 1.0) and confirmed the speed of AutoDock Vina. Afterwards, the lowest-energy conformer of each molecule and all the conformers lying 0-10 kcal/mol above it (as given by Macrocycle, from MacroModel 10.0) were subjected to standard docking calculations...
January 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28105916/gpcrs-from-fusarium-graminearum-detection-modeling-and-virtual-screening-the-search-for-new-routes-to-control-head-blight-disease
#6
Emmanuel Bresso, Roberto Togawa, Kim Hammond-Kosack, Martin Urban, Bernard Maigret, Natalia Florencio Martins
BACKGOUND: Fusarium graminearum (FG) is one of the major cereal infecting pathogens causing high economic losses worldwide and resulting in adverse effects on human and animal health. Therefore, the development of new fungicides against FG is an important issue to reduce cereal infection and economic impact. In the strategy for developing new fungicides, a critical step is the identification of new targets against which innovative chemicals weapons can be designed. As several G-protein coupled receptors (GPCRs) are implicated in signaling pathways critical for the fungi development and survival, such proteins could be valuable efficient targets to reduce Fusarium growth and therefore to prevent food contamination...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28104810/the-foxp2-forkhead-domain-binds-to-a-variety-of-dna-sequences-with-different-rates-and-affinities
#7
Helen Webb, Olga Steeb, Ashleigh Blane, Lia Rotherham, Shaun Aron, Phillip Machanick, Heini Dirr, Sylvia Fanucchi
FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA binding domain of which is the winged helix forkhead domain. In this work we show that the FOXP2 forkhead domain is able to bind to various DNA sequences, including a novel sequence identified in this work, with different affinities and rates as detected using surface plasmon resonance. Combining the experimental work with molecular docking, we show that high affinity sequences remain bound to the protein for longer, form a greater number of interactions with the protein and induce a greater structural change in the protein than low affinity sequences...
January 18, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28103689/structure-and-function-of-a-c-c-bond-cleaving-oxygenase-in-atypical-angucycline-biosynthesis
#8
Guohui Pan, Xiaoqin Gao, Keqiang Fan, Junlin Liu, Bing Meng, Jinmin Gao, Bin Wang, Chaobo Zhang, Hui Han, Guomin Ai, Yihua Chen, Dong Wu, Zhi-Jie Liu, Keqian Yang
C-C bond ring cleaving oxygenases represent a unique family of enzymes involved in the B ring cleavage reaction only observed in atypical angucycline biosynthesis. B ring cleavage is the key reaction leading to dramatic divergence in the final structures of atypical angucyclines. Here, we present the crystal structure of AlpJ, the first structure of this family of enzymes. AlpJ has been verified as the enzyme catalyzing C-C bond cleavage in kinamycin biosynthesis. The crystal structure of the AlpJ monomer resembles the dimeric structure of ferredoxin-like proteins...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28103683/simultaneous-targeting-of-npc1-and-vdac1-by-itraconazole-leads-to-synergistic-inhibition-of-mtor-signaling-and-angiogenesis
#9
Sarah A Head, Wei Q Shi, Eun Ju Yang, Benjamin A Nacev, Sam Y Hong, Kalyan K Pasunooti, Ruo-Jing Li, Joong Sup Shim, Jun O Liu
The antifungal drug itraconazole was recently found to exhibit potent antiangiogenic activity and has since been repurposed as an investigational anticancer agent. Itraconazole has been shown to exert its antiangiogenic activity through inhibition of the mTOR signaling pathway, but the molecular mechanism of action was unknown. We recently identified the mitochondrial protein VDAC1 as a target of itraconazole and a mediator of its activation of AMPK, an upstream regulator of mTOR. However, VDAC1 could not account for the previously reported inhibition of cholesterol trafficking by itraconazole, which was also demonstrated to lead to mTOR inhibition...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28100778/structure-of-the-z-ring-associated-protein-zapd-bound-to-the-c-terminal-domain-of-the-tubulin-like-protein-ftsz-suggests-mechanism-of-z-ring-stabilization-through-ftsz-crosslinking
#10
Maria Schumacher, Kuo-Hsiang Huang, Wenjie Zeng, Anuradha Janakiraman
Cell division in most bacteria is mediated by the tubulin-like FtsZ protein, which polymerizes in a GTP-dependent manner to form the cytokinetic Z ring. A diverse repertoire of FtsZ binding proteins affect FtsZ localization and polymerization to ensure correct Z ring formation. Many of these proteins bind the C-terminal domain (CTD) of FtsZ, which serves as a hub for FtsZ regulation. FtsZ ring-associated proteins, ZapA-D (Zaps), are important FtsZ regulatory proteins that stabilize FtsZ assembly and enhance Z ring formation by increasing lateral assembly of FtsZ protofilaments, which then form the Z ring...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100636/centriole-splitting-caused-by-loss-of-the-centrosomal-linker-protein-c-nap1-reduces-centriolar-satellite-density-and-impedes-centrosome-amplification
#11
Anne-Marie Flanagan, Elena Stavenschi, Shivakumar Basavaraju, David Gaboriau, David A Hoey, Ciaran G Morrison
Duplication of the centrosomes is a tightly regulated process. Abnormal centrosome numbers can impair cell division and cause changes in how cells migrate. Duplicated centrosomes are held together by a proteinaceous linker made up of rootletin filaments anchored to the centrioles by C-NAP1. This linker is removed in a NEK2A kinase-dependent manner as mitosis begins. To explore C-NAP1 activities in regulating centrosome activities, we used genome editing to ablate it. C-NAP1 null cells were viable and had an increased frequency of premature centriole separation, accompanied by reduced density of the centriolar satellites, with re-expression of C-NAP1 rescuing both these phenotypes...
January 18, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28100206/hypoglycemic-effects-of-trichosanthes-kirilowii-and-its-protein-constituent-in-diabetic-mice-the-involvement-of-insulin-receptor-pathway
#12
Hsin-Yi Lo, Tsai-Chung Li, Tse-Yen Yang, Chia-Cheng Li, Jen-Huai Chiang, Chien-Yun Hsiang, Tin-Yun Ho
BACKGROUND: Diabetes is a serious chronic metabolic disorder. Trichosanthes kirilowii Maxim. (TK) is traditionally used for the treatment of diabetes in traditional Chinese medicine (TCM). However, the clinical application of TK on diabetic patients and the hypoglycemic efficacies of TK are still unclear. METHODS: A retrospective cohort study was conducted to analyze the usage of Chinese herbs in patients with type 2 diabetes in Taiwan. Glucose tolerance test was performed to analyze the hypoglycemic effect of TK...
January 18, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28100093/p19-targeted-abd-derived-protein-variants-inhibit-il-23-binding-and-exert-suppressive-control-over-il-23-stimulated-expansion-of-primary-human-il-17-t-cells
#13
Lucie Křížová, Milan Kuchař, Hana Petroková, Radim Osička, Marie Hlavničková, Ondřej Pelák, Jiří Černý, Tomáš Kalina, Petr Malý
Interleukin-23 (IL-23), a heterodimeric cytokine of covalently bound p19 and p40 proteins, has recently been closely associated with development of several chronic autoimmune diseases such as psoriasis, psoriatic arthritis or inflammatory bowel disease. Released by activated dendritic cells, IL-23 interacts with IL-23 receptor (IL-23R) on Th17 cells, thus promoting intracellular signaling, a pivotal step in Th17-driven pro-inflammatory axis. Here, we aimed to block the binding of IL-23 cytokine to its cell-surface receptor by novel inhibitory protein binders targeted to the p19 subunit of human IL-23...
January 19, 2017: Autoimmunity
https://www.readbyqxmd.com/read/28099027/inactivation-of-soybean-trypsin-inhibitor-by-epigallocatechin-gallate-stopped-flow-fluorescence-thermodynamics-and-docking-studies
#14
Chun Liu, Fenfen Cheng, Xiaoquan Yang
Tea is one of the most widely daily consumed beverages all over the world, and it is usually consumed with milk and/or soy milk. However, very few researches have studied the interactions between tea polyphenols (TPs) and soy milk proteins as compared with milk proteins. Here, we reported that epigallocatechin gallate (EGCG), a major component of TPs, can effectively inhibit the inhibitory activity of Kunitz trypsin inhibitor (KTI, a major antinutrient in soy milk). The mechanism of inactivation of KTI by EGCG was investigated by stopped-flow/fluorescence, thermodynamics, and docking studies...
January 18, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28097901/skin-whitening-agents-medicinal-chemistry-perspective-of-tyrosinase-inhibitors
#15
Thanigaimalai Pillaiyar, Manoj Manickam, Vigneshwaran Namasivayam
Melanogenesis is a process to synthesize melanin, which is a primary responsible for the pigmentation of human skin, eye and hair. Although numerous enzymatic catalyzed and chemical reactions are involved in melanogenesis process, the enzymes such as tyrosinase and tyrosinase-related protein-1 (TRP-1) and TRP-2 played a major role in melanin synthesis. Specifically, tyrosinase is a key enzyme, which catalyzes a rate-limiting step of the melanin synthesis, and the downregulation of tyrosinase is the most prominent approach for the development of melanogenesis inhibitors...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28097462/thermally-stable-schiff-base-and-its-metal-complexes-molecular-docking-and-protein-binding-studies
#16
Umran Duru Kamaci, Musa Kamaci, Aysegul Peksel
In this paper, interaction of Schiff base and its metal complexes carrying naphthalene ring in the structure with bovine serum albumin (BSA) were investigated using UV-vis absorption, fluorescence spectroscopies and molecular docking methods. The effect on the binding mechanism and properties of these compounds containing metal-free, iron and copper ions were also investigated. The fluorescence spectroscopy results showed that fluorescence intensity of BSA in the presence of different concentration of ligands was decreased through a static quenching mechanism...
January 18, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28097460/synthesis-spectral-characterization-dna-protein-binding-dna-cleavage-cytotoxicity-antioxidative-and-molecular-docking-studies-of-cu-ii-complexes-containing-schiff-base-bpy-phen-ligands
#17
Berelli Anupama, Airva Aruna, Vijjulatha Manga, Sreekanth Sivan, Madamsetty Vijay Sagar, Ravula Chandrashekar
Ternary Cu(II) complexes [Cu(II)(L)(bpy)Cl] 1, [Cu(II)(L)(Phen)Cl] 2 [L = 2,3-dimethyl-1-phenyl-4(2 hydroxy-5-methyl benzylideneamino)-pyrazol-5-one, bpy = 2,2(') bipyridine, phen =1,10 phenanthroline) were synthesized and characterized by elemental analyses, UV-Visible, FT-IR, ESR, Mass, thermogravimetric and SEM EDAX techniques. The complexes exhibit octahedral geometry. The interaction of the Cu(II) with cailf thymus DNA (CT-DNA) was explored by using absorption and fluorescence spectroscopic methods...
January 17, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28096388/competition-of-calcified-calmodulin-n-lobe-and-pip2-to-an-lqt-mutation-site-in-kv7-1-channel
#18
William Sam Tobelaim, Meidan Dvir, Guy Lebel, Meng Cui, Tal Buki, Asher Peretz, Milit Marom, Yoni Haitin, Diomedes E Logothetis, Joel Alan Hirsch, Bernard Attali
Voltage-gated potassium 7.1 (Kv7.1) channel and KCNE1 protein coassembly forms the slow potassium current IKS that repolarizes the cardiac action potential. The physiological importance of the IKS channel is underscored by the existence of mutations in human Kv7.1 and KCNE1 genes, which cause cardiac arrhythmias, such as the long-QT syndrome (LQT) and atrial fibrillation. The proximal Kv7.1 C terminus (CT) binds calmodulin (CaM) and phosphatidylinositol-4,5-bisphosphate (PIP2), but the role of CaM in channel function is still unclear, and its possible interaction with PIP2 is unknown...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096188/erk1-2-phosphorylate-gab2-to-promote-a-negative-feedback-loop-that-attenuates-pi3k-akt-signaling
#19
Xiaocui Zhang, Geneviève Lavoie, Antoine Méant, Léo Aubert, Marie Cargnello, André Haman, Trang Hoang, Philippe P Roux
The scaffolding adapter protein Gab2 (Grb2-associated binder) promotes cell proliferation, survival and motility by engaging several signaling pathways downstream of growth factor and cytokine receptors. In particular, Gab2 plays essential roles in mast cells as it is required for PI3K (phosphoinositide 3-kinase) activation in response to Kit and the high-affinity IgE receptor. While the positive role of Gab2 in PI3K signaling is well documented, very little is known about the mechanisms that attenuate its function...
January 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28094221/synthesis-biological-evaluation-and-molecular-docking-analysis-of-2-phenyl-benzofuran-3-carboxamide-derivatives-as-potential-inhibitors-of-staphylococcus-aureus-sortase-a
#20
Wan He, Yong Zhang, Jian Bao, Xinxian Deng, Jennifer Batara, Shawn Casey, Qiuyuan Guo, Faqin Jiang, Lei Fu
In Gram-positive bacteria, Sortase A (Srt A) is a critical cysteine transpeptidase that is responsible for recognizing and assembling surface virulence proteins through the recognition of a LPXTG (leucine, proline, X, threonine, and glycine, where X is any amino acid) signal. Mutants lacking genes for Srt A attenuate infections without affecting microbial viability. Here a series of 2-phenyl-benzofuran-3-carboxamide derivatives were synthesized and identified as potent Srt A inhibitors. Activity assays revealed that multiple compounds exhibited excellent inhibitory activity against Srt A compared with known Sortase A inhibitor pHMB (IC50=130μM)...
December 25, 2016: Bioorganic & Medicinal Chemistry
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