Read by QxMD icon Read

Journal of Molecular Graphics & Modelling

Benedetta Righino, Angelo Minucci, Davide Pirolli, Ettore Capoluongo, Giorgio Conti, Daniele De Luca, Maria Cristina De Rosa
Phospholipase A2-IIA catalyzes the hydrolysis of the sn-2 ester of glycerophospholipids. A rare c.428G > A (p.Arg143His) variant in PLA2G2A gene was found in two infants affected by acute respiratory distress syndrome (ARDS) by whole coding region and exon/intron boundaries sequencing. To obtain insights into the possible molecular effects of the rare R123H mutation in secretory PLA2-IIA (sPLA2-IIA), molecular modelling, molecular dynamics (MD) using principal component analysis (PCA) and continuum electrostatic calculations were conducted on the crystal structure of the wild type protein and on a generated model structure of the R123H mutant...
March 6, 2018: Journal of Molecular Graphics & Modelling
Saeideh Tasharrofi, Hossein Taghdisian, Abdollah Golchoobi
In this study, pure and ternary adsorption of hydrogen sulfide (H2 S), ethylbenzene (EB), and carbon monoxide (CO) on different arrays of zigzag double wall carbon nanotube was investigated using grand canonical Monte Carlo simulations. The internal diameters of nanotube were fixed at 2r = 50.17 Å while nanotube wall distances were different values from d = 0 Å to d = 150 Å. Pure simulation results indicated that adsorption quantity of H2 S and EB in low pressure ranges of P = 1.9 bar to P = 3...
March 2, 2018: Journal of Molecular Graphics & Modelling
Xueping Hu, Bin Yin, Kaat Cappelle, Luc Swevers, Guy Smagghe, Xinling Yang, Li Zhang
Insect growth is regulated by the steroid hormone 20-hydroxyecdysone (20E), which works via the ecdysone receptor (EcR). To identify biologically active and novel ecdysone agonists/antagonists, ligand/structure-based virtual screening combined with pharmacophore modeling and molecular docking was performed to identify novel nonsteroidal lead compounds. Nine molecules were screened and selected for an in vitro cell-based reporter bioassay. The results showed that VS-006 and VS-009 exhibited antagonistic activity in S2 cells, whereas only VS-006 exhibited antagonistic activity in Bm5 cells...
March 2, 2018: Journal of Molecular Graphics & Modelling
Zahra Rostami, Akram Hosseinian, Aazam Monfared
Some electronic properties of different C60 and C70 derivatives were evaluated using 20 density functionals (the B3LYP, BHANDH, PBE0, HSE06, CAM-B3LYP, ωB97X-D, BMK, PBEPBE, M06-L, M06, M06-2X, M06-HF, PW91PW91, BLYP, B97D, HCT407, τ-HCTH, τ-HCTHhyb, TPSS, and LSDA), and some of the results were compared with the available experimental data. Unlike in Hartree-Fock (HF) method, the orbital relaxation is not the origin of the violation of DFT from the Koopmans' theorem. For most of functionals, the HOMO-LUMO gap (Eg ) is more sensitive to the functional compared to the optical gap...
March 2, 2018: Journal of Molecular Graphics & Modelling
Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha
This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain...
March 2, 2018: Journal of Molecular Graphics & Modelling
Hiqmet Kamberaj
In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method...
February 22, 2018: Journal of Molecular Graphics & Modelling
Shabbir Muhammad, Abdullah G Al-Sehemi, Ahmad Irfan, H Algarni, Yongqing Qiu, Hongliang Xu, Zhongmin Su, Javed Iqbal
The present study spotlights the hybrid chalcone derivatives consisting of coumarin moieties conjugated systematically with different heterocyclic rings. The heterocyclic rings including bifuran, bicyclopentane, bipyrrole and bithiophenes groups are used to design compounds 1, 2, 3 and 4, respectively. Different density functional theory (DFT) methods are used for optimization of designed compounds. The M06 functional shows reasonably good accuracy for calculations of geometrical and absorption spectra as compared with other methods and/or available experimental data...
February 13, 2018: Journal of Molecular Graphics & Modelling
Mahmoud A Al-Sha'er, Mutasem O Taha
Akt1 and Akt3 are important serine/threonine-specific protein kinases involved in G2 phase required by cancer cells to maintain cell cycle and to prevent cell death. Accordingly, inhibitors of these kinases should have potent anti-cancer properties. This prompted us to use pharmacophore/QSAR modeling to identify optimal binding models and physicochemical descriptors that explain bioactivity variation within a set of 74 diverse Akt3 inhibitors. Two successful orthogonal pharmacophores were identified and further validated using receiver operating characteristic (ROC) curve analyses...
February 13, 2018: Journal of Molecular Graphics & Modelling
Emmanuel Amoah Boafo, Kwabena Darko, Bright Aryeh Afriyie, Richard Tia, Evans Adei
The mechanistic aspects of cycloaddition reactions of 1,2-cyclohexadiene with olefins and nitrones have been investigated with DFT calculations. The results show that the cycloaddition reactions of 1,2-cyclohexadiene with olefins do not go through a concerted pathway (one-step mechanism) but rather a stepwise one involving the formation of a biradical intermediate which then closes to form final cycloadduct. Electron-withdrawing substituents on the 1,2-cyclohexadiene decrease the activation barrier of the biradical-forming step but increase the barrier of the product-forming step and product stability, while electron-donating substituents on the 1,2-cyclohexadiene increase the barriers for both the biradical-forming step and the product-forming step but decrease the product stability...
February 13, 2018: Journal of Molecular Graphics & Modelling
Karthikeyan Muthusamy, Selvaraman Nagamani
Pharmacogenetics and pharmacogenomics have become presumptive with advancements in next-generation sequencing technology. In complex diseases, distinguishing the feasibility of pathogenic and neutral disease-causing variants is a time consuming and expensive process. Recent drug research and development processes mainly rely on the relationship between the genotype and phenotype through Single nucleotide polymorphisms (SNPs). The SNPs play an indispensable role in elucidating the individual's vulnerability to disease and drug response...
February 12, 2018: Journal of Molecular Graphics & Modelling
P Popov, S Grudinin
Conformational ensembles comprise one of the fundamental concepts in statistical bioinformatics and appear in a variety of applications, e.g. molecular docking, virtual screening, searching for pharmacophores, etc. High-throughput applications require billions of conformations to be considered, thus, one often uses the rigid-body representation of molecules or its fragments to cope with the computational cost. Of particular interest is generation of the near-native conformational ensembles, which consist of conformations structurally close to the biologically relevant ones...
February 2, 2018: Journal of Molecular Graphics & Modelling
Robert D Barrows, Kristin M Blacklock, Paul R Rablen, Sagar D Khare, Spencer Knapp
Replacement of the sulfur atom in biologically active diaryl and heteroaryl thioethers (Ar-S-Ar', HAr-S-Ar, and HAr-S-HAr') with any of several one-atom or two-atom linkers can be expected to reduce the susceptibility of the analogue to metabolic oxidation, a well-documented problem for thioethers intended for medicinal chemistry applications. Ab initio calculations indicate how well various proposed thioether isosteric groups, including some new and unusual ones, may perform structurally and electronically in replacing the bridging sulfur atom...
February 1, 2018: Journal of Molecular Graphics & Modelling
Ryosuke Takeda, Ittetsu Kobayashi, Rie Suzuki, Kentaro Kawai, Atsushi Kittaka, Midori Takimoto-Kamimura, Noriyuki Kurita
Vitamin D plays an important role in the regulation of the calcium and phosphorus metabolism as well as in bone formation. These physiological actions caused by vitamin D are triggered by the specific binding of vitamin D to its receptor (VDR). Here we investigated the specific interactions and binding affinities between VDR and vitamin D derivatives, using ab initio fragment molecular orbital (FMO) calculations. The FMO results elucidate that relative position of the two hydroxyl groups of the derivatives is essential for the strong binding affinity between the derivative and Arg274 residue of VDR...
January 31, 2018: Journal of Molecular Graphics & Modelling
Shize Liu, Lin Cheng, Kai Li, Ying Wang, Yuewen Yang, Zhijian Wu
The transition metal and nitrogen co-doped graphene as efficient electrocatalysts of oxygen reduction reaction (ORR) is promising to achieve large-scale applications of the full cells. In this work, we investigated the active sites and ORR mechanism on IrN4 doped divacancy graphene (IrN4-Gra) by using the density functional method. The active sites are identified as the IrN4 moiety and its adjacent ten C atoms. ORR on IrN4-Gra is a four-electron process. OOH hydrogenated into OH + OH is the kinetically most favorable pathway...
January 31, 2018: Journal of Molecular Graphics & Modelling
J M Martínez-Magadán, A R Cartas-Rosado, R Oviedo-Roa, R Cisneros-Dévora, M Pons-Jiménez, R Hernández-Altamirano, L S Zamudio-Rivera
Branched gemini zwitterionic liquids, which contain two zwitterionic moieties of linked quaternary-ammonium and carboxylate groups, are proposed as chemicals to be applied in the Enhanced Oil Recovery (EOR) from fractured carbonate reservoirs. The zwitterionic moieties are bridged between them through an alkyl chain containing 12 ether groups, and each zwitterionic moiety has attached a long alkyl tail including a CC double bond. A theoretical molecular mechanism over which EOR could rest, consisting on both the disaggregation of heavy oil and the reservoir-rock wettability alteration, was suggested...
January 31, 2018: Journal of Molecular Graphics & Modelling
Yelda Asad, Sajjad Ahmad, Thanyada Rungrotmongkol, Kara E Ranaghan, Syed Sikander Azam
The bacterium Providencia stuartii, is associated with urinary tract infections and is the most common cause of purple urine bag syndrome. The increasing multi-drug resistance pattern shown by the pathogen and lack of licensed vaccines make treatment of infections caused by P. stuartii challenging. As vaccinology data against the pathogen is scarce, an in silico proteome based Reverse Vaccinology (RV) protocol, in combination with subtractive proteomics is introduced in this work to screen potential vaccine candidates against P...
January 31, 2018: Journal of Molecular Graphics & Modelling
Rosana M Lobayan, María Celia Pérez Schmit
Serotonin (5-hydroxytryptamine, SER) is a neurotransmitter that affects many different processes within the human body. We studied the conformational space of SER, and explored in depth the significant stereoelectronic features for the structure stabilization and antioxidant activity. Forty-eight equilibrium structures were described at the B3LYP/6-311++G(d,p) level, characterizing four non-previously reported conformers. Electron distributions were analyzed by topological QTAIM (Quantum Theory of atoms in molecules) and natural bond orbital (NBO) studies...
January 31, 2018: Journal of Molecular Graphics & Modelling
Rui-Juan Zhuang, Wei-Dong Jin, Xiao-Yan Wang, Xue-Ming Wu
Olmesartan (OL) is the pharmacologically active metabolite of Olmesartan medoxomil (OM), an FDA-approved angiotensin II receptor antagonist for administrating cardiovascular diseases. The drug has been found to have potential effects on diverse protein kinase signaling involved in the pathogenesis of atherosclerosis, either by directly inhibiting the hub kinases or by indirectly modulating marginal members in the signaling pathways. In the present study, we computationally model the kinase-chemical Interaction Profile between six OL-related chemicals (i...
January 30, 2018: Journal of Molecular Graphics & Modelling
Sadegh Kaviani, Mohammad Izadyar, Mohammad Reza Housaindokht
The chelating agents for Al3+ and Fe3+ metal cations with therapeutic applications have been considered in the recent years. In designing of the hydroxypyridinones (HPOs) as the therapeutic chelating agents for iron and aluminium overload pathologies, quantum mechanical (QM) calculations are necessary for predicting the binding energies and thermodynamic parameters of the metal-HPO complexes. Three derivatives of the HPOs called 3-hydroxy-1,2-dimethylpyridin-4(1H)-one (DFP), 3-hydroxy-4(1H)-pyridinone (HOPO) and 5-hydroxy-2-(hydroxymethyl)pyridin-4(1H)-one (P1) were investigated for complexation with Fe3+ and Al3+ metal ions...
January 29, 2018: Journal of Molecular Graphics & Modelling
S Amirhossein Tabatabaei-Dakhili, Rodrigo Aguayo-Ortiz, Laura Domínguez, Carlos A Velázquez-Martínez
The FOXM1 protein is a relevant transcription factor involved in cancer cell proliferation. The direct or indirect inhibition of this protein's transcriptional activity by small molecule drugs correlates well with a potentially significant anti-cancer profile, making this macro molecule a promising drug target. There are a few drug molecules reported to interact with (and inhibit) the FOXM1 DNA binding domain (FOXM1-BD), causing downregulation of protein expression and cancer cell proliferation inhibition. Among these drug molecules are the proteasome inhibitor thiostrepton, the former antidiabetic drug troglitazone, and the new FDI-6 molecule...
January 27, 2018: Journal of Molecular Graphics & Modelling
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"