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https://www.readbyqxmd.com/read/29156382/discovery-of-selective-dengue-virus-inhibitors-using-combination-of-molecular-fingerprint-based-virtual-screening-protocols-structure-based-pharmacophore-model-development-molecular-dynamics-simulations-and-in-vitro-studies
#1
Shaher Bano Mirza, Regina Ching Hua Lee, Justin Jang Hann Chu, Ramin Ekhteiari Salmas, Thomas Mavromoustakos, Serdar Durdagi
Dengue virus is a major issue of tropical and sub-tropical regions. The proliferation of virus results in immense number of deaths each year because of unavailability of on-shelf drugs. This issue necessitates the design of novel anti-Dengue drugs. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of Dengue virus. Keeping in mind the worsening situation regarding Dengue virus, approximately eighteen million drug-like compounds from the ZINC small molecule database have been screened against Nonstructural Protein 3 (NS3) previously by our group...
October 24, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29155905/adsorption-of-three-domain-antifreeze-proteins-on-ice-a-study-using-lgmmas-theory-and-monte-carlo-simulations
#2
Juan Ignacio Lopez Ortiz, Paola Torres, Evelina Quiroga, Claudio F Narambuena, Antonio J Ramirez-Pastor
In the present work, the adsorption of three-domain antifreeze proteins on ice is studied by combining a statistical thermodynamics based theory and Monte Carlo simulations. The three-domain protein is modeled by a trimer, and the ice surface is represented by a lattice of adsorption sites. The statistical theory, obtained from the exact partition function of non-interacting trimers adsorbed in one dimension and its extension to two dimensions, includes the configuration of the molecule in the adsorbed state, and allows the existence of multiple adsorption states for the protein...
November 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29155876/docking-analysis-and-the-possibility-of-prediction-efficacy-for-an-anti-il-13-biopharmaceutical-treatment-with-tralokinumab-and-lebrikizumab-for-bronchial-asthma
#3
Yutaka Nakamura, Aki Sugano, Mika Ohta, Yutaka Takaoka
Interleukin-13 (IL-13) is associated with allergic airway inflammation and airway remodeling. Our group found a variant with a single nucleotide polymorphism in the IL13 gene at position +2044G>A (rs20541) that was expected to result in the non-conservative replacement of a positively charged arginine (R) with a neutral glutamine (Q) at position 144. IL-13Q144 was associated with augmented allergic airway inflammation and bronchial asthma remodeling. There is some indication that anti-IL-13 monoclonal antibodies can demonstrate a positive effect on the clinical course of refractory asthmatic patients...
2017: PloS One
https://www.readbyqxmd.com/read/29155158/thermodynamic-investigation-of-an-alkaline-protease-from-aspergillus-tamarii-urm4634-a-comparative-approach-between-crude-extract-and-purified-enzyme
#4
Osmar Soares da Silva, Rodrigo Lira de Oliveira, Jonatas de Carvalho Silva, Attilio Converti, Tatiana Souza Porto
The thermostable crude proteolytic extract and purified protease produced by Aspergillus tamarii URM4634 were investigated at different temperatures. The activity results were used to estimate the activation energy of the hydrolysis reaction catalyzed by crude extract and purified protease (E*=34.2 and 16.2kJ/mol) as well as the respective standard enthalpy variations of reversible enzyme unfolding (ΔH°u=31.9 and 13.9kJ/mol). When temperature was raised from 50 to 80°C in residual activity tests, the specific rate constant of crude proteolytic extract thermoinactivation increased from 0...
November 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29155106/monomerization-and-aggregation-of-%C3%AE-lactoglobulin-under-adverse-condition-a-fluorescence-correlation-spectroscopic-investigation
#5
Bhaswati Sengupta, Nilimesh Das, Pratik Sen
β-lactoglobulin is one of the major components of bovine milk and it remains in a dimeric form under physiological conditions. The present contribution elucidates the structural change of β-lactoglobulin at pH7.4 under the action of guanidine hydrochloride (GnHCl) and heat at the single molecular level. The only free cysteine (Cys-121) of β-lactoglobulin has been tagged with 7-Diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM) for this purpose. The dimeric structure of β-lactoglobulin found to undergoes a monomerization prior to the unfolding process upon being subjected to GnHCl...
November 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29154687/pyruvate-enhancement-of-cardiac-performance-cellular-mechanisms-and-clinical-application
#6
Robert T Mallet, Albert H Olivencia-Yurvati, Rolf Bünger
Cardiac contractile function is adenosine-5'-triphosphate (ATP)-intensive, and the myocardium's high demand for oxygen and energy substrates leaves it acutely vulnerable to interruptions in its blood supply. The myriad cardioprotective properties of the natural intermediary metabolite pyruvate make it a potentially powerful intervention against the complex injury cascade ignited by myocardial ischemia-reperfusion. A readily oxidized metabolic substrate, pyruvate augments myocardial free energy of ATP hydrolysis to a greater extent than the physiological fuels glucose, lactate and fatty acids, particularly when it is provided at supra-physiological plasma concentrations...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29154164/molecular-insights-into-inclusion-complexes-of-mansonone-e-and-h-enantiomers-with-various-%C3%AE-cyclodextrins
#7
Panupong Mahalapbutr, Bodee Nutho, Peter Wolschann, Warinthorn Chavasiri, Nawee Kungwan, Thanyada Rungrotmongkol
The structural dynamics and stability of inclusion complexes of mansonone E (ME) and H (MH) including their stereoisomers with various βCDs (methylated- and hydroxypropylated-βCDs) were investigated by classical molecular dynamics (MD) simulations and binding free energy calculations. The simulation results revealed that mansonones are able to form inclusion complexes with βCDs. The guest molecules are not completely inserted into the host cavity, their preferably positions are nearby the secondary rim with the oxane ring dipping into the hydrophobic inner cavity...
November 11, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29153891/molecular-modeling-of-cationic-porphyrin-anthraquinone-hybrids-as-dna-topoisomerase-ii%C3%AE-inhibitors
#8
Muhammad Arba, Ruslin, Sunandar Ihsan, Setyanto Tri Wahyudi, Daryono H Tjahjono
Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14...
October 5, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153883/conformational-dynamics-and-free-energy-of-bhrf1-binding-to-bim-bh3
#9
Mauro Lapelosa
The interaction between the Bim BH3 peptide and the viral protein BHRF1 is pivotal to understanding the fundamental molecular details of the mechanism used by the Epstein-Barr virus to trick the mammalian immune system. Here, we study the mechanism of binding/unbinding and compute the free energy for the association of the Bim peptide to the BHRF1 protein. Key elements of the binding mechanism are the conformational rearrangement together with a main free energy barrier of 11.5kcal/mol. The simulations show complete unbinding and rebinding of the Bim peptide to BHRF1...
November 10, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29151344/computation-of-hemagglutinin-free-energy-difference-by-the-confinement-method
#10
Sander Boonstra, Patrick R Onck, Erik Van der Giessen
Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results...
November 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29150461/gabaa-receptor-activation-in-the-allosteric-coagonist-model-framework-relationship-between-ec50-and-basal-activity
#11
Gustav Akk, Daniel J Shin, Allison L Germann, Joseph H Steinbach
The concerted transition model for multimeric proteins is a simple formulation for analyzing the behavior of transmitter-gated ion channels. Here, we use the model to examine the relationship between the EC50 for activation of the GABAA receptor by the transmitter GABA and basal activity employing concatemeric ternary GABAA receptors expressed in Xenopus oocytes. The basal activity reflects receptor function in the absence of transmitter, and can be changed either by mutation to increase constitutive activity, or by addition of a second agonist (acting at a different site) to increase background activity...
November 17, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/29149637/antiviral-potential-of-natural-compounds-against-influenza-virus-hemagglutinin
#12
S Kannan, P Kolandaivel
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29146980/the-energy-cost-of-polypeptide-knot-formation-and-its-folding-consequences
#13
Andrés Bustamante, Juan Sotelo-Campos, Daniel G Guerra, Martin Floor, Christian M A Wilson, Carlos Bustamante, Mauricio Báez
Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain-an event that can potentially impair its folding-and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol(-1). Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29144736/inference-of-calmodulin-s-ca2-dependent-free-energy-landscapes-via-gaussian-mixture-model-validation
#14
Annie M Westerlund, Tyler J Harpole, Christian Blau, Lucie Delemotte
A free energy landscape estimation-method based on the well-known Gaussian mixture model (GMM) is used for comparing the efficiency of thermally enhanced sampling methods with respect to regular molecular dynamics. The simulations are carried out on two binding states of calmodulin and the free energy estimation method is compared to other estimators using a toy model. We show that GMM with cross-validation provides a robust estimate that is not subject to overfitting. The continuous nature of Gaussians provides better estimates on sparse data than canonical histogramming...
November 16, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29144135/parameterization-of-palmitoylated-cysteine-farnesylated-cysteine-geranylgeranylated-cysteine-and-myristoylated-glycine-for-the-martini-force-field
#15
Yoav Atsmon-Raz, D Peter Tieleman
Peripheral membrane proteins go through various post-translational modifications that covalently bind fatty acid tails to specific amino acids. These post translational modifications significantly alter the lipophilicity of the modified proteins and allow them to anchor to biological membranes. Over 1000 different proteins have been identified to date that require such membrane-protein interactions in order to carry out their biological functions, including members of the Src and Ras superfamilies that play key roles in cell signaling and carcinogenesis...
November 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29144001/biological-evaluation-and-energetic-analyses-of-novel-gsk-3%C3%AE-inhibitors
#16
Denan Zhang, Lei Liu, Lin Pang, Qing Jin, Kehui Ke, Ming Hu, Jingbo Yang, Weifang Ma, Hongbo Xie, Xiujie Chen
Glycogen synthase kinase-3 beta (GSK-3β) is involved in multiple signaling pathways. Consistent with its critical roles in normal cells, abnormalities in GSK-3β activity have been implicated in diabetes, heart disease, Parkinson disease and Alzheimer's disease. In this study, a series of new scaffolds of small molecule inhibitors of GSK-3β were identified by virtual screening and bioassay. Candidates that adhere to drug-like criteria from a virtual library of compounds were tested using computational docking studies...
November 16, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29143527/origins-of-enantioselectivity-in-asymmetric-radical-additions-to-octahedral-chiral-at-rhodium-enolates-a-computational-study
#17
Shuming Chen, Xiaoqiang Huang, Eric Meggers, Kendall N Houk
The origin of asymmetric induction in the additions of carbon- and nitrogen-centered radicals to octahedral centrochiral rhodium enolates has been investigated with Density Functional Theory (DFT) calculations. Computed free energies of activation reproduce the preference for the experimentally observed major enantiomer. Good levels of enantioselectivity are maintained upon replacement of the bulky tert-butyl substituents on the ligands with methyl groups. Distortion-interaction analysis indicates that for both carbon-and nitrogen-centered radicals, which have relatively early and late transition states, respectively, the difference in the distortion energies controls the enantioselectivity...
November 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29143152/electrochemical-and-theoretical-studies-of-the-interactions-of-a-pyridyl-based-corrosion-inhibitor-with-iron-clusters-fe15-fe30-fe45-and-fe60
#18
Julian Cruz-Borbolla, Esteban Garcia-Ochoa, Jayanthi Narayanan, Pablo Maldonado-Rivas, Thangarasu Pandiyan, José M Vásquez-Pérez
The capacity of 2,6-bis[((2-pyridylmethyl)oxy)methyl)]pyridine (BPMMP) to inhibit the corrosion of mild carbon steel in HCl was analyzed. In a polarization study, both the cathodic and anodic currents were appreciably decreased in the presence of BPMMP, suggesting that this ligand is effective at inhibiting corrosion at the metal surface. This conclusion is consistent with the results of impedance analysis, where only one time constant corresponding to one depressed capacitive loop was detected, and the diameter of the impedance plot was directly related to the concentration of BPMMP...
November 15, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29143031/acid-base-machines-electrical-work-from-neutralization-reactions
#19
Gilberto Lima, William G Morais, Wellington J A S Gomes, Fritz Huguenin
We have developed an electrochemical system that performs electrical work due to changes in alkaline ion and proton activities associated with acidic solution neutralization. This system can be used to treat wastewater, contributing to sustainable growth. The system includes an electrochemical machine that operates between an acidic and a basic reservoir to produce work in cycles comprising four stages: two isothermal ionic insertion/de-insertion steps and two steps involving acid and base injection. On the basis of the mixing free energy associated with the reaction free energy, we have developed the thermodynamic formalism by considering reversible electrochemical processes to determine the maximum work performed by this acid-base machine and the efficiency...
November 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29142407/molecular-docking-analysis-of-phytic-acid-and-4-hydroxyisoleucine-as-cyclooxygenase-2-microsomal-prostaglandin-e-synthase-2-tyrosinase-human-neutrophil-elastase-matrix-metalloproteinase-2-and-9-xanthine-oxidase-squalene-synthase-nitric-oxide-synthase-human
#20
Radhakrishnan Narayanaswamy, Lam Kok Wai, Norhaizan Mohd Esa
Background: The phytoconstituents phytic acid and 4-hydroxyisoleucine have been reported to posses various biological properties. Objective: This prompted us to carry out the docking study on these two ligands (phytic acid & 4-hydroxyisoleucine) against eleven targeted enzymes. Materials and Methods: Phytic acid & 4-hydroxyisoleucine were evaluated on the docking behaviour of cyclooxygenase-2 (COX-2), microsomal prostaglandin E synthase-2 (mPGES-2), tyrosinase, human neutrophil elastase (HNE), matrix metalloproteinase (MMP 2 and 9), xanthine oxidase (XO), squalene synthase (SQS), nitric oxide synthase (NOS), human aldose reductase (HAR) and lipoxygenase (LOX) using Discovery Studio Version 3...
October 2017: Pharmacognosy Magazine
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