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https://www.readbyqxmd.com/read/28550736/piperine-attenuates-uv-r-induced-cell-damage-in-human-keratinocytes-via-nf-kb-bax-bcl-2-pathway-an-application-for-photoprotection
#1
Ankit Verma, Hari N Kushwaha, Ajeet K Srivastava, Saumya Srivastava, Naseem Jamal, Kriti Srivastava, Ratan Singh Ray
Chronic ultraviolet radiation (UV-R) exposure causes skin disorders like erythema, edema, hyperpigmentation, photoaging and photocarcinogenesis. Recent research trends of researchers have focused more attention on the identification and use of photo stable natural agents with photoprotective properties. Piperine (PIP), as a plant alkaloid, is an important constituent present in black pepper (Piper nigrum), used widely in ayurvedic and other traditional medicines and has broad pharmacological properties. The study was planned to photoprotective efficacy of PIP in human keratinocyte (HaCaT) cell line...
May 19, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28548833/structure-activity-relationship-for-small-molecule-inhibitors-of-nicotinamide-n-methyltransferase
#2
Harshini Neelakantan, Hua-Yu Wang, Virginia Vance, Jonathan D Hommel, Stanton F McHardy, Stanley J Watowich
Nicotinamide N-methyltransferase (NNMT) is a fundamental cytosolic biotransforming enzyme that catalyzes the N-methylation of endogenous and exogenous xenobiotics. We have identified small molecule inhibitors of NNMT with >1000-fold range of activity and developed comprehensive structure-activity relationships (SARs) for NNMT inhibitors. Screening of N-methylated quinolinium, isoquinolinium, pyrididium, and benzimidazolium/benzothiazolium analogs resulted in the identification of quinoliniums as a promising scaffold with very low micromolar (IC50 ~1 μM) NNMT inhibition...
May 26, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28548666/zinc-and-the-iron-donor-frataxin-regulate-oligomerization-of-the-scaffold-protein-to-form-new-fe-s-cluster-assembly-centers
#3
B K Galeano, W Ranatunga, O Gakh, D Y Smith, J R Thompson, G Isaya
Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1...
May 26, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28546827/chemical-constituents-from-a-gynostemma-laxum-and-their-antioxidant-and-neuroprotective-activities
#4
Ji Yeon Seo, Sang Kyum Kim, Phi Hung Nguyen, Ju Yong Lee, Pham Ha Thanh Tung, Sang Hyun Sung, Won Keun Oh
BACKGROUND: A few bioactivities of constituents from Gynostemma laxum, which has been collected in Vietnam, have been reported until now. There is no report about the effects of constituents from G. laxum although the nuclear factor (erythroid-derived 2)-like 2 (Nrf2)-mediated heme oxygenase-1 (HO-1) antioxidant defense system is involved in neuroprotection in the brain. Therefore, we investigated whether quercetin (2), benzoic acid (10) and their analogues (1, 3-9 and 11) from G. laxum have the antioxidant and neuroprotective activities and also their underlying mechanism...
2017: Chinese Medicine
https://www.readbyqxmd.com/read/28545576/a-computational-assessment-of-ph-dependent-differential-interaction-of-t7-lysozyme-with-t7-rna-polymerase
#5
Subhomoi Borkotoky, Ayaluru Murali
BACKGROUND: T7 lysozyme (T7L), also known as N-acetylmuramoyl-L-alanine amidase, is a T7 bacteriophage gene product. It involves two functions: It can cut amide bonds in the bacterial cell wall and interacts with T7 RNA polymerase (T7RNAP) as a part of transcription inhibition. In this study, with the help of molecular dynamics (MD) calculations and computational interaction studies, we investigated the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions...
May 25, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28544778/differential-regulation-of-protein-tyrosine-kinase-signaling-by-dock-and-the-ptp61f-variants
#6
Lee F Willoughby, Jan Manent, Kirsten Allan, Han Lee, Marta Portela, Florian Wiede, Coral Warr, Tzu-Ching Meng, Tony Tiganis, Helena E Richardson
Tyrosine phosphorylation-dependent signalling is coordinated by the opposing actions of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). There is a growing list of adaptor proteins that interact with PTPs and facilitate the dephosphorylation of substrates. The extent to which any given adaptor confers selectivity for any given substrate in vivo remains unclear. Here we have taken advantage of Drosophila melanogaster as a model organism to explore the influence of the SH3/SH2 adaptor protein Dock on the abilities of the membrane (PTP61Fm)- and nuclear (PTP61Fn)-targeted variants of PTP61F (the Drosophila othologue of the mammalian enzymes PTP1B and TCPTP respectively) to repress PTK signaling pathways in vivo...
May 23, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28543724/predicting-binding-modes-of-reversible-peptide-based-inhibitors-of-falcipain-2-consistent-with-structure-activity-relationships
#7
Jorge Enrique Hernández González, Lilian Hernández Alvarez, Pedro Geraldo Pascutti, Pedro Alberto Valiente
Falcipain-2 (FP-2) is a major hemoglobinase of Plasmodium falciparum, considered an important drug target for the development of antimalarials. A previous study reported a novel series of twenty reversible peptide-based inhibitors of FP-2. However, the lack of tridimensional structures of the complexes hinders further optimization strategies to enhance the inhibitory activity of the compounds. Here we report the prediction of the binding modes of the aforementioned inhibitors to FP-2. A computational approach combining previous knowledge on the determinants of binding to the enzyme, docking and post-docking refinement steps, is employed...
May 24, 2017: Proteins
https://www.readbyqxmd.com/read/28541224/protein-protein-interaction-interface-residue-pair-prediction-based-on-deep-learning-architecture
#8
Zhenni Zhao, Xinqi Gong
MOTIVATION: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interaction between two monomer proteins. The correct prediction of interface residue pairs from two monomer proteins is still an open question and has great significance for practical experimental applications in the life sciences. We hope to build a method for the prediction of interface residue pairs that is suitable for those applications...
May 19, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28541222/drug-target-prediction-by-multi-view-low-rank-embedding
#9
Limin Li, Menglan Cai
Drug repositioning has been a key problem in drug development, and heterogeneous data sources are used to predict drug-target interactions by different approaches. However, most of studies focus on a single representation of drugs or proteins. It has been shown that integrating multi-view representations of drugs and proteins can strengthen the prediction ability. For example, a drug can be represented by its chemical structure, or by its chemical response in different cells. A protein can be represented by its sequence, or by its gene expression values in different cells...
May 18, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28540166/inhibition-of-protein-kinases-by-anticancer-dna-intercalator-4-butylaminopyrimido-4-5-4-5-thieno-2-3-b-quinoline
#10
HeggoduG Rohit Kumar, Chethan S Kumar, Hulihalli N Kiran Kumar, Gopal M Advi Rao
Targeting protein kinases (PKs) has been a promising strategy in treating cancer, as PKs are key regulators of cell survival and proliferation. Here in this study, we studied the ability of pyrimido[4',5':4,5]thieno(2,3-b)quinolines (PTQ) to inhibit different PKs by performing computational docking and in vitro screening. Docking studies revealed that 4-butylaminopyrimido[4',5':4,5]thieno(2,3-b)quinoline (BPTQ) has a higher order of interaction with the kinase receptors than other PTQ derivatives. In vitro screening confirms that BPTQ inhibits VEGFR1 and CHK2, with the IC50 values of 0...
May 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28539733/molecular-docking-of-phytoligands-to-the-viral-protein-receptor-p-monodon-rab7
#11
Jerrine Joseph, Raj Bhaskaran, Muthusamy Kaliraj, Muthiyah Muthuswamy, Arumugam Suresh
The development of shrimp aquaculture has been severely affected by viral diseases resulting in a huge economic burden to the industry. White spot disease (WSD) has caused severe mortality in farmed shrimp in many countries. Globally aquaculture industries face huge economic losses due to rapid spread of White Spot Syndrome Virus (WSSV) disease that can cause 100% mortality in a short period of 3-10 days. In the present study in order to prevent the spread of WSSV disease in shrimps, the receptor, PmRab7 has been chosen as the drug target...
2017: Bioinformation
https://www.readbyqxmd.com/read/28539432/golgi-associated-protein-kinase-c-%C3%AE%C2%B5-is-delivered-to-phagocytic-cups-role-of-phosphatidylinositol-4-phosphate
#12
Cheryl M Hanes, Anna E D'Amico, Takehiko Ueyama, Alexander C Wong, Xuexin Zhang, W Frederick Hynes, Margarida M Barroso, Nathaniel C Cady, Mohamed Trebak, Naoaki Saito, Michelle R Lennartz
Protein kinase C-ε (PKC-ε) at phagocytic cups mediates the membrane fusion necessary for efficient IgG-mediated phagocytosis. The C1B and pseudosubstrate (εPS) domains are necessary and sufficient for this concentration. C1B binds diacylglycerol; the docking partner for εPS is unknown. Liposome assays revealed that the εPS binds phosphatidylinositol 4-phosphate (PI4P) and PI(3,5)P2 Wortmannin, but not LY294002, inhibits PKC-ε concentration at cups and significantly reduces the rate of phagocytosis. As Wortmannin inhibits PI4 kinase, we hypothesized that PI4P mediates the PKC-ε concentration at cups and the rate of phagocytosis...
May 24, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28539360/a-dock-and-coalesce-mechanism-driven-by-hydrophobic-interactions-governs-cdc42-binding-with-its-effector-protein-ack
#13
George J N Tetley, Helen R Mott, R Neil Cooley, Darerca Owen
Cdc42 is a Rho-family small G protein that has been widely studied for its role in controlling the actin cytoskeleton and plays a part in several potentially oncogenic signalling networks. Similar to most other small G proteins, Cdc42 binds to many downstream effector proteins to elicit its cellular effects. These effector proteins all engage the same face of Cdc42, the conformation of which is governed by the activation state of the G protein. Previously, the importance of individual residues in conferring binding affinity has been explored for residues within Cdc42 for three of its CRIB effectors, activated Cdc42 kinase (ACK), p21-activated kinase (PAK), and Wiskott-Aldrich syndrome protein (WASP)...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28537140/molecular-modeling-driven-approach-for-identification-of-janus-kinase-1-inhibitors-through-3d-qsar-docking-and-molecular-dynamics-simulations
#14
Ramesh Itteboina, Srilata Ballu, Sree Kanth Sivan, Vijjulatha Manga
Janus kinase 1 (JAK 1) belongs to the JAK family of intracellular nonreceptor tyrosine kinase. JAK-signal transducer and activator of transcription (JAK-STAT) pathway mediate signaling by cytokines, which control survival, proliferation and differentiation of a variety of cells. Three-dimensional quantitative structure activity relationship (3 D-QSAR), molecular docking and molecular dynamics (MD) methods was carried out on a dataset of Janus kinase 1(JAK 1) inhibitors. Ligands were constructed and docked into the active site of protein using GLIDE 5...
May 24, 2017: Journal of Receptor and Signal Transduction Research
https://www.readbyqxmd.com/read/28536001/membrane-shaping-by-actin-and-myosin-during-regulated-exocytosis
#15
REVIEW
Andreas Papadopulos
The cortical actin network in neurosecretory cells is a dense mesh of actin filaments underlying the plasma membrane. Interaction of actomyosin with vesicular membranes or the plasma membrane is vital for tethering, retention, transport as well as fusion and fission of exo- and endocytic membrane structures. During regulated exocytosis the cortical actin network undergoes dramatic changes in morphology to accommodate vesicle docking, fusion and replenishment. Most of these processes involve plasma membrane Phosphoinositides (PIP) and investigating the interactions between the actin cortex and secretory structures has become a hotbed for research in recent years...
May 20, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/28534194/assessing-protein-ligand-binding-modes-with-computational-tools-the-case-of-pde4b
#16
Gülşah Çifci, Viktorya Aviyente, E Demet Akten, Gerald Monard
In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects, we present a protocol to rank newly designed molecules through the estimation of their IC[Formula: see text] values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC[Formula: see text] values [[Formula: see text](IC[Formula: see text])] and their calculated binding free energies ([Formula: see text]). From 13 known PDE4B inhibitors, we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship; (2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationship; (3) by taking into account all representative structures obtained by AutoDock and by averaging MM-GB/SA computations on a series of 40 independent MD trajectories, a linear relationship between [Formula: see text](IC[Formula: see text]) and the lowest [Formula: see text] is achieved with [Formula: see text]...
May 22, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28533752/protocatechuic-acid-a-phenolic-from-sansevieria-roxburghiana-leaves-suppresses-diabetic-cardiomyopathy-via-stimulating-glucose-metabolism-ameliorating-oxidative-stress-and-inhibiting-inflammation
#17
Niloy Bhattacharjee, Tarun K Dua, Ritu Khanra, Swarnalata Joardar, Ashis Nandy, Achintya Saha, Vincenzo De Feo, Saikat Dewanjee
Persistent hyperglycemia, impairment of redox status and establishment of inflammatory pathophysiology integrally play important role in the pathogenesis of diabetic cardiomyopathy (DC). Present study examined the therapeutic potential of protocatechuic acid isolated from the Sansevieria roxburghiana rhizomes against DC employing rodent model of type 2 diabetes (T2D). T2D was induced by high fat diet + a low-single dose of streptozotocin (35 mg/kg, i.p.). T2D rats exhibited significantly (p < 0.01) high fasting blood glucose level...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28533339/structure-based-prediction-of-wnt-binding-affinities-for-frizzled-type-cysteine-rich-domain
#18
Mark Agostino, Sebastian Öther-Gee Pohl, Arunasalam Dharmarajan
Wnt signaling pathways are of significant interest in development and oncogenesis. The first step in these pathways typically involves the binding of a Wnt protein to the cysteine-rich domain (CRD) of a Frizzled receptor; Wnt-Frizzled interactions can be antagonized by secreted Frizzled-related proteins (sFRPs), which also contain a Frizzled-like CRD. The large number of Wnts, Frizzleds and sFRPs, as well as the hydrophobic nature of Wnt, pose challenges to laboratory-based investigations of interactions involving Wnt...
May 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28532672/molecular-insights-into-the-differences-in-anti-inflammatory-activities-of-green-tea-catechins-on-il-1%C3%AE-signaling-in-rheumatoid-arthritis-synovial-fibroblasts
#19
Sabrina Fechtner, Anil Singh, Mukesh Chourasia, Salahuddin Ahmed
In this study, we found that catechins found in green tea (EGCG, EGC, and EC) differentially interfere with the IL-1β signaling pathway which regulates the expression of pro-inflammatory mediators (IL-6 and IL-8) and Cox-2 in primary human rheumatoid arthritis synovial fibroblasts (RASFs). EGCG and EGC inhibited IL-6, IL-8, and MMP-2 production and selectively inhibited Cox-2 expression. EC did not exhibit any inhibitory effects. When we looked at the expression of key signaling proteins in the IL-1β signaling pathway, we found all the tested catechins could inhibit TAK-1 activity...
May 19, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28531794/binding-of-the-anticancer-drug-bi-2536-to-human-serum-albumin-a-spectroscopic-and-theoretical-study
#20
Jesús Fernández-Sainz, Pedro J Pacheco-Liñán, José M Granadino-Roldán, Iván Bravo, Andrés Garzón, Jaime Rubio-Martínez, José Albaladejo
BI-2536 is a potent Polo-like kinase inhibitor which induces apoptosis in diverse human cancer cell lines. The binding affinity of BI-2536 for human serum albumin (HSA) protein may define its pharmacokinetic and pharmacodynamic profile. We have studied the binding of BI-2536 to HSA by means of different spectroscopic techniques and docking calculations. We have experimentally observed that the affinity of BI-2536 for HSA is higher than that of other common HSA binding drugs. Therefore, it can be postulated that the drug dose should be increased to achieve a certain concentration of free drug in plasma, although BI-2536 could also reach tumour tissues by uptaking HSA/BI-2536 complex...
May 12, 2017: Journal of Photochemistry and Photobiology. B, Biology
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