keyword
MENU ▼
Read by QxMD icon Read
search

Protein-protein docking

keyword
https://www.readbyqxmd.com/read/29223569/isolated-mangiferin-and-naringenin-exert-antidiabetic-effect-via-ppar%C3%AE-glut4-dual-agonistic-action-with-strong-metabolic-regulation
#1
Ashok K Singh, Vinit Raj, Amit K Keshari, Amit Rai, Pranesh Kumar, Atul Rawat, Biswanath Maity, Dinesh Kumar, Anand Prakash, Arnab De, Amalesh Samanta, Bolay Bhattacharya, Sudipta Saha
In this study, we isolated two compounds from the leaves of Salacia oblonga (SA1, mangiferin and SA2, naringenin), and their structures were confirmed by infrared spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry. SA1 and SA2 were orally administered to streptozotocin-induced diabetic rats at 50 and 100 mg/kg daily for 15 days. Blood glucose level, serum lipid profile, oxidative stress parameters, histopathology, docking, molecular parameters, and NMR-based metabolic perturbation studies were performed to investigate the pharmacological activities of SA1 and SA2...
December 6, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/29223460/investigation-of-anticancer-properties-of-caffeinated-complexes-via-computational-chemistry-methods
#2
Koray Sayin, Ayhan Üngördü
Computational investigations were performed for 1,3,7-trimethylpurine-2,6-dione, 3,7-dimethylpurine-2,6-dione, their Ru(II) and Os(III) complexes. B3LYP/6-311++G(d,p)(LANL2DZ) level was used in numerical calculations. Geometric parameters, IR spectrum, 1H-, 13C and 15N NMR spectrum were examined in detail. Additionally, contour diagram of frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) maps, MEP contour and some quantum chemical descriptors were used in the determination of reactivity rankings and active sites...
December 6, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29222162/dual-inhibition-of-pik3c3-and-fgfr-as-a-new-therapeutic-approach-to-treat-bladder-cancer
#3
Chun-Han Chen, C Changou, Tsung-Han Hsieh, Yu-Ching Lee, Cheng-Ying Chu, Kai-Cheng Hsu, Hao-Ching Wang, Yu-Chen Lin, Yan-Ni Lo, Yun-Ru Liu, Jing-Ping Liou, Yun Yen
PURPOSE: MPT0L145 has been developed as a FGFR inhibitor exhibiting significant anti-bladder cancer activity in vitro and in vivo via promoting autophagy-dependent cell death. Here, we aim to elucidate the underlying mechanisms. EXPERIMENTAL DESIGN: Autophagy flux, morphology and intracellular organelles were evaluated by western blotting, transmission electron microscope and fluorescence microscope. Molecular docking, surface plasmon resonance assay were performed to identify drug-protein interaction...
December 8, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29221906/presynaptic-active-zones-of-mammalian-neuromuscular-junctions-nanoarchitecture-and-selective-impairments-in-aging
#4
REVIEW
Yomna Badawi, Hiroshi Nishimune
Neurotransmitter release occurs at active zones, which are specialized regions of the presynaptic membrane. A dense collection of proteins at the active zone provides a platform for molecular interactions that promote recruitment, docking, and priming of synaptic vesicles. At mammalian neuromuscular junctions (NMJs), muscle-derived laminin β2 interacts with presynaptic voltage-gated calcium channels to organize active zones. The molecular architecture of presynaptic active zones has been revealed using super-resolution microscopy techniques that combine nanoscale resolution and multiple molecular identification...
December 5, 2017: Neuroscience Research
https://www.readbyqxmd.com/read/29221464/molecular-and-functional-characterization-of-ferredoxin-nadp-h-oxidoreductase-from-gracilaria-chilensis-and-its-complex-with-ferredoxin
#5
María Alejandra Vorphal, Carola Bruna, Traudy Wandersleben, Jorge Dagnino-Leone, Francisco Lobos-González, Elena Uribe, José Martínez-Oyanedel, Marta Bunster
BACKGROUD: Ferredoxin NADP(H) oxidoreductases (EC 1.18.1.2) (FNR) are flavoenzymes present in photosynthetic organisms; they are relevant for the production of reduced donors to redox reactions, i.e. in photosynthesis, the reduction of NADP+ to NADPH using the electrons provided by Ferredoxin (Fd), a small FeS soluble protein acceptor of electrons from PSI in chloroplasts. In rhodophyta no information about this system has been reported, this work is a contribution to the molecular and functional characterization of FNR from Gracilaria chilensis, also providing a structural analysis of the complex FNR/Fd...
December 8, 2017: Biological Research
https://www.readbyqxmd.com/read/29221189/novel-direct-ampk-activator-suppresses-non-small-cell-lung-cancer-through-inhibition-of-lipid-metabolism
#6
Xi Chen, Chun Xie, Xing-Xing Fan, Ze-Bo Jiang, Vincent Kam-Wai Wong, Jia-Hui Xu, Xiao-Jun Yao, Liang Liu, Elaine Lai-Han Leung
Drug resistance is becoming an obstacle in anti-cancer therapies. For target-based therapy of lung cancer, gefitinib, as the first generation of tyrosine kinase inhibitors (TKIs), demonstrated good initial response to the non-small cell lung cancer (NSCLC) patients whom harbors epidermal growth factor receptor (EGFR) mutation. However, within one year, additional EGFR mutation occurred, leading to eventual gefitinib-resistance. Therefore, it is urgently to discover novel effective small molecule inhibitors for those patients...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221149/prediction-on-the-risk-population-of-idiosyncratic-adverse-reactions-based-on-molecular-docking-with-mutant-proteins
#7
Hongbo Xie, Diheng Zeng, Xiujie Chen, Diwei Huo, Lei Liu, Denan Zhang, Qing Jin, Kehui Ke, Ming Hu
Idiosyncratic adverse drug reactions are drug reactions that occur rarely and unpredictably among the population. These reactions often occur after a drug is marketed, which means that they are strongly related to the genotype of the population. The prediction of such adverse reactions is a major challenge because of the lack of appropriate test models during the drug development process. In this study, we chose withdrawn drugs because the reasons why they were withdrawn and from which countries or regions is easily obtained...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29218563/a-practical-guide-to-ispot-modeling-an-integrative-structural-biology-platform
#8
An Hsieh, Lanyuan Lu, Mark R Chance, Sichun Yang
Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques. Here, we provide a practical protocol for implementing our integrated iSPOT platform by integrating three different biophysical techniques: small-angle X-ray scattering (SAXS), hydroxyl radical footprinting, and computational docking simulations. Specifically, individual techniques are described from experimental and/or computational perspectives, and complementary structural information from these different techniques are integrated for accurate characterization of the structures of large protein-protein complexes...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29218430/cpdock-the-complementarity-plot-for-docking-of-proteins-implementing-multi-dielectric-continuum-electrostatics
#9
Sankar Basu
The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or interface and plots them in a two-dimensional plot having knowledge-based probabilistic quality estimates for the residues as well as for the whole structure. The current report essentially presents an upgraded version of the plot with the implementation of the advanced multi-dielectric functionality (as in Delphi version 6...
December 7, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29216799/flavonoids-as-potent-allosteric-inhibitors-of-protein-tyrosine-phosphatase-1b-molecular-dynamics-simulation-and-free-energy-calculation
#10
Farshid Zargari, Maryam Lotfi, Omolbanin Shahraki, Zahra Nikfarjam, Jafar Shahraki
Protein tyrosine phosphatase 1B (PTP1B) is a member of the PTP superfamily which is considered to be a negative regulator of insulin receptor (IR) signalling pathway. PTP1B is a promising drug target for the treatment of type 2 diabetes, obesity and cancer. The existence of allosteric site in PTP1B has turned the researcher's attention to an alternate strategy for inhibition of this enzyme. Herein, the molecular interactions between the allosteric site of PTP1B with three non-competitive flavonoids, (MOR), (MOK), and (DPO) have been investigated...
December 7, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29216011/understanding-the-molecular-mechanism-of-improved-proliferation-and-osteogenic-potential-of-human-mesenchymal-stem-cells-grown-on-a-polyelectrolyte-complex-derived-from-non-mulberry-silk-fibroin-and-chitosan
#11
Akalabya Bissoyi, Abhishek Kumar Singh, Subrat Kumar Pattanayak, Arindam Bit, Sudip Kumar Sinha, Ashish Patel, Vishal Jain, Pradeep Kumar Patra
The development of engineered bone tissue, as a promising alternative to conventional bone grafts, has so far not proven successful and still remains challenging. Thus, attempts have been made in the present study to synthesize polyelectrolyte complex (PEC) scaffolds by blending chitosan (CS) to silk fibroin (SF) derived from the non-mulberry silkworm (Antheraea pernyi) at three different pH values (5.0, 6.0, and 7.0), and to characterize them in terms of morphology, ultrastructure and mechanical properties with scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy, x-ray diffraction and tensile strength analyses...
December 7, 2017: Biomedical Materials
https://www.readbyqxmd.com/read/29215703/design-synthesis-and-characterization-of-%C3%AE-%C3%AE-unsaturated-carboxylic-acid-and-its-urea-based-derivatives-that-explores-novel-epigenetic-modulators-in-human-non-small-cell-lung-cancer-a549-cell-line
#12
Anusha Chidambaram, S H Kavya, Ramesh Kumar Chidambaram, Rajasekaran Subbiah, John Marshal Jayaraj, Karthikeyan Muthusamy, Ravikumar Vilwanathan
Histone deacetylase inhibitors (HDACi) are a small molecule chemotherapeutics that target the chromatin remodeling through the regulation of histone and non-histone proteins. These inhibitors directed against HDAC enzymes have become an important therapeutic tool in oncology; consequently, scientific efforts have fortified the quest for newer and novel HDACi, which forces the design of structurally innovative HDACi. Various urea containing compounds exhibited admirable anticancer activity. On the basis of these observations, we design and synthesize HDAC specific blocker molecules which are specifically besieged towards class I, class II and class IV HDAC isoforms to enhance the structural assortment for HDACi...
December 7, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29215184/a-single-mutation-increases-the-activity-and-stability-of-pectobacterium-carotovorum-nitrile-reductase
#13
Zheng Zhou, Min Li, Jian-He Xu, Zhi-Jun Zhang
Nitrile reductase is considered as a promising and environmentally benign nitrile-reducing biocatalyst to replace traditional metal catalysts. Unfortunately, the catalytic efficiencies of nitrile reductases reported so far are very low. To date, any attempts by protein engineering to increase the catalytic activity of nitrile reductase have failed. In this work, we successfully increased the specific activity of a nitrile reductase from Pectobacterium carotovorum from 354 U·gprot-1 to 526 U·gprot-1 by engineering the substrate binding pocket, meanwhile the thermostability was also improved (ca...
December 7, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29212707/inherent-steroid-17%C3%AE-20-lyase-activity-in-defunct-cytochrome-p450-17a-enzymes
#14
Eric Gonzalez, Kevin M Johnson, Pradeep S Pallan, Thanh T N Phan, Wei Zhang, L I Lei, Zdzislaw Wawrzak, Francis K Yoshimoto, Martin Egli, F Peter Guengerich
Cytochrome P450 (P450) 17A1 catalyzes the oxidations of progesterone and pregnenolone and is the major source of androgens. The enzyme catalyzes both 17α-hydroxylation and a subsequent 17α, 20-lyase reaction, and several mechanisms have been proposed for the latter step. Zebrafish P450 17A2 catalyzes only the 17α-hydroxylations. We previously reported high similarity of the crystal structures of zebrafish P450 17A1 and 17A2 and human P450 17A1 (Pallan et al. (2015) J. Biol. Chem. 290, 3248- 3268). Five residues near the heme, which differed, were changed...
December 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29212526/structural-and-functional-annotation-of-hypothetical-proteins-of-human-adenovirus-prioritizing-the-novel-drug-targets
#15
Muhammad Naveed, Sana Tehreem, Muhammad Usman, Zoma Chaudhry, Ghulam Abbas
OBJECTIVE: Human adenoviruses are small double stranded DNA viruses that provoke vast array of human diseases. Next generation sequencing techniques increase genomic data of HAdV rapidly, which increase their serotypes. The complete genome sequence of human adenovirus shows that it contains large amount of proteins with unknown cellular or biochemical function, known as hypothetical proteins. Hence, it is indispensable to functionally and structurally annotate these proteins to get better understanding of the novel drug targets...
December 6, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29211993/single-molecule-study-reveals-how-receptor-and-ras-synergistically-activate-pi3k%C3%AE-and-pip3-signaling
#16
Thomas C Buckles, Brian P Ziemba, Glenn R Masson, Roger L Williams, Joseph J Falke
Cellular pathways controlling chemotaxis, growth, survival, and oncogenesis are activated by receptor tyrosine kinases and small G-proteins of the Ras superfamily that stimulate specific isoforms of phosphatidylinositol-3-kinase (PI3K). These PI3K lipid kinases phosphorylate the constitutive lipid phosphatidylinositol-4,5-bisphosphate (PIP2) to produce the signaling lipid phosphatidylinositol-3,4,5-trisphosphate (PIP3). Progress has been made in understanding direct, moderate PI3K activation by receptors. In contrast, the mechanism by which receptors and Ras synergistically activate PI3K to much higher levels remains unclear, and two competing models have been proposed: membrane recruitment versus activation of the membrane-bound enzyme...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29211985/the-rna-binding-site-of-poliovirus-3c-protein-doubles-as-a-phosphoinositide-binding-domain
#17
Djoshkun Shengjuler, Yan Mei Chan, Simou Sun, Ibrahim M Moustafa, Zhen-Lu Li, David W Gohara, Matthias Buck, Paul S Cremer, David D Boehr, Craig E Cameron
Some viruses use phosphatidylinositol phosphate (PIP) to mark membranes used for genome replication or virion assembly. PIP-binding motifs of cellular proteins do not exist in viral proteins. Molecular-docking simulations revealed a putative site of PIP binding to poliovirus (PV) 3C protein that was validated using nuclear magnetic resonance spectroscopy. The PIP-binding site was located on a highly dynamic α helix, which also functions in RNA binding. Broad PIP-binding activity was observed in solution using a fluorescence polarization assay or in the context of a lipid bilayer using an on-chip, fluorescence assay...
December 5, 2017: Structure
https://www.readbyqxmd.com/read/29211957/binding-mechanisms-of-electron-transport-proteins-with-cyanobacterial-photosystem-i-an-integrated-computational-and-experimental-model
#18
Karan Kapoor, Derek J Cashman, Luke Nientimp, Barry D Bruce, Jerome Yves Baudry
The stromal domain (PsaC, D, and E) of photosystem I (PSI) in Cyanobacteria accepts electrons from PsaA and PsaB of photosystem I (PSI). These electrons then reduce transiently bound ferredoxin (Fd) or flavodoxin. Experimental structures exist for all of these protein partners individually, yet to date, no experimental structure of the PSI/Fd complexes is presently available. Molecular models of Fd docked into the stromal domain of the cyanobacterial PSI site are constructed here starting from X-ray and NMR structures of PSI and Fd...
December 6, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29211037/in-silico-identification-and-in-vitro-evaluation-of-natural-inhibitors-of-leishmania-major-pteridine-reductase-i
#19
Fabian C Herrmann, Nirina Sivakumar, Joachim Jose, Maria P Costi, Cecilia Pozzi, Thomas J Schmidt
In a continuation of our computational efforts to find new natural inhibitors of a variety of target enzymes from parasites causing neglected tropical diseases (NTDs), we now report on 15 natural products (NPs) that we have identified as inhibitors of Leishmania major pteridine reductase I (LmPTR1) through a combination of in silico and in vitro investigations. Pteridine reductase (PTR1) is an enzyme of the trypanosomatid parasites' peculiar folate metabolism, and has previously been validated as a drug target...
December 6, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29210581/modelling-of-human-fatty-acid-synthase-and-in-silico-docking-of-acyl-carrier-protein-domain-and-its-partner-catalytic-domains
#20
Rui P P Neves, Maria João Ramos, Pedro A Fernandes, Matilde Viegas
Human Fatty Acid Synthase (hFAS) is a megasynthase whose main function is de novo biosynthesis of saturated fatty acids. Interest has been drawn to this enzyme beyond its physiological role due to the association between high levels of hFAS and clinical conditions such as obesity, diabetes and cancer. Thus, it has become an undeniably attractive pharmacological target. Until now, no crystal structure of the complete hFAS is available, hindering attempts to fully understand this protein. Using homology modelling, we built a model of the entire megasynthase, encompassing all of its domains, including the Acyl Carrier Protein (ACP) and Thioesterase (TE) mobile domains absent in the crystal structure of mammalian Fatty Acid Synthase (FAS)...
December 6, 2017: Journal of Physical Chemistry. B
keyword
keyword
13117
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"