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Journal of Molecular Graphics & Modelling

Nikolay A Alemasov, Nikita V Ivanisenko, Bhupesh Taneja, Vibha Taneja, Srinivasan Ramachandran, Vladimir A Ivanisenko
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease characterised by the inevitable degeneration of central and peripheral motor neurons. Aggregation of mutant SOD1 is one of the molecular mechanisms underlying the onset of the disease. There are a number of regression models designed to predict the survival of patients based on an analysis of experimental data on thermostability, heterodimerisation energy, and changes in the hydrophobicity of SOD1 mutants. Previously, we proposed regression models linking the change in the stability of hydrogen bonds in mutant SOD1 calculated using molecular dynamics and elastic networks with patients survival time...
November 1, 2018: Journal of Molecular Graphics & Modelling
Marian Verdes
Hydrates of HCl, HNO3 and H2 SO4 involved in polar stratospheric clouds capture the attention of researchers due to the mixtures composed with them. The molecular aggregates generated with these strong acids show different behaviors, geometries and nucleation reactions at atmospheric temperatures. Here is presented a systematic ab initio optimization study of monohydrates of HCl•HNO3 •H2 SO4 using the Density Functional Theory, by means of geometry optimizations carried out with B3LYP hybrid method and aug-cc-pVTZ basis set, a high level of theory, within Gaussian 09 program...
October 31, 2018: Journal of Molecular Graphics & Modelling
Marjan A Nejad, Herbert M Urbassek
The diffusion and adsorption behavior of cisplatin in silica nanopores is investigated using molecular dynamics simulation. Two different silica conformations are studied in order to characterize the influence of surface polarity and inner pore wall structure. Acceleration techniques are used in order to sample adsorption phase space efficiently. We find a strong influence of the pore diameter on the diffusion coefficient; only for pore diameters larger than roughly 1.6 nm, cisplatin assumes a comparable diffusion coefficient as in bulk water...
October 25, 2018: Journal of Molecular Graphics & Modelling
Farnaz Jahanbin, Mohammad Reza Bozorgmehr, Ali Morsali, S Ali Beyramabadi
The beta-amyloid peptide Aβ1-42 is the most effective peptide in the process of forming plaque and creating Alzheimer's. After the separation of Aβ1-42 from APP membrane protein, the membrane surface is transmitted to the extracellular environment, which is a crowded environment. On the other hand, stability of salt bridges Asp23-Lys28 and Lys28-Ala42 is important for monomer toxicity and fibrillation formation. In this work, the effects of ethanol, propanol, butanol, pentanol, hexanol, heptanol and octanol on the Asp23-Lys28 and Lys28-Ala42 salt bridges of the Aβ1-42 have been investigated by molecular dynamics simulation...
October 23, 2018: Journal of Molecular Graphics & Modelling
Yao-Bing Yin, Qiu-Sheng Yang, Shu-Ling Wang, Hui-Dong Gao, Yong-Wu He, Xiao-Liang Li
The epoxy resin coating is a fundamental species with epoxy resins used as main components to form the final film. Unexpectedly, bulky CO2 bubbles that occasionally appeared during the curing process of epoxy resin coatings might destroy the final film properties. With an attempt to thoroughly understand the formation mechanism of CO2 bubbles and further propose countermeasures to control them, Density Function Theory (DFT) in this paper was employed to calculate the absorption process, the curing reaction and the formation mechanism of CO2 bubbles...
October 23, 2018: Journal of Molecular Graphics & Modelling
Ephraim Muriithi Kiarii, Krishna Kuben Govender, Messai Adenew Mamo, Penny Poomani Govender
Two-dimensional TiSe2 , with Yb14 MnSb11 and AlSb9 Yb11 thermoelectric materials, were used to generate heterostructures. The electronic and optical calculations were done using the Materials Studio 2018 modelling software package, employing the Cambridge Serial Total Energy Package code and using the generalised gradient approximation with Perdew-Burke-Ernzerhof exchange-correlation functionals. However, the electronic results obtained revealed a reduction in the calculated band gap and an increase in the slope of the density of state at the Femi level, as well as the energy bands of the generated heterostructures was reported...
October 22, 2018: Journal of Molecular Graphics & Modelling
Paige N Castleman, Chandler K Sears, Judith A Cole, Daniel L Baker, Abby L Parrill
G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for drug development. GPCR ligand interaction studies often have a starting point with either crystal structures or comparative models. The majority of GPCR do not have experimentally-characterized 3-dimensional structures, so comparative modeling, also called homology modeling, is a good structure-based starting point. Comparative modeling is a widely used method for generating models of proteins with unknown structures by analogy to crystallized proteins that are expected to exhibit structural conservation...
October 21, 2018: Journal of Molecular Graphics & Modelling
Süleyman Selim Çınaroğlu, Emel Timuçin
Replication Protein A (RPA) mediates DNA Damage Response (DDR) pathways through protein-protein interactions (PPIs). Targeting the PPIs formed between RPA and other DNA Damage Response (DDR) mediators has become an intriguing area of research for cancer drug discovery. A number of studies applied different methods ranging from high throughput screening approaches to fragment-based drug design tools to discover RPA inhibitors. Although these methods are robust, virtual screening approaches may be allocated as an alternative to such experimental methods, especially for screening of large libraries...
October 20, 2018: Journal of Molecular Graphics & Modelling
Yunyuan Huang, Bo Chi, Yanhong Xu, Rongrong Song, Lin Wei, Li Rao, Lingling Feng, Yanliang Ren, Jian Wan
Fructose-1, 6-bisphosphatase (FBPase) has been regarded as an attractive drug target to control blood glucose against Type 2 diabetes (T2D). In this study, by using the strategy of pharmacophore-based virtual screening, a novel scaffold inhibitor targeted the AMP allosteric site of human liver FBPase were screened, their inhibitory activities were further tested. The experimental results showed that compound H27 exhibited high inhibitory activities with the IC50 value of 5.3 μM. Therefore, compound H27 was chosen as the probe molecule, it's possible binding conformation targeted into FBPase was identified by using DOX2...
October 20, 2018: Journal of Molecular Graphics & Modelling
Amina S Aljaber, Abdulilah Dawoud Bani-Yaseen
The characterization of potential tautomerization of pharmaceutical materials has significant importance. Sulfasalazine (SSZ) is a prodrug that bears 5-aminosalicylic acid and pyridylamino-sulfonyl-phenyl moieties bridged by the azo group. SSZ may be present in various tautomeric forms, where dual tautomerization may occur; namely, amide↔imide and azo↔hydrazone tautomerization through the pyridylamino-sulfonyl-phenyl and salicylic acid moieties, respectively. In this report, we describe the prospects of the effect of molecular medium on the tautomerization of SSZ using selected computational methods...
October 19, 2018: Journal of Molecular Graphics & Modelling
Maicol Ahumedo Monterrosa, Johan Fabian Galindo, Javier Vergara Lorduy, Jorge Alí-Torres, Ricardo Vivas-Reyes
The present work combines molecular docking calculations, 3D-QSAR, molecular dynamics simulations and free binding energy calculations (MM/PBSA and MM/GBSA) in a set of 28 structural analogues of acyl homoserine lactones with Quorum Sensing antagonist activity. The aim of this work is to understand how ligand binds and is affected by the molecular microenvironment in the active site of the LasR receptor for pseudomonas aeruginosa. We also study the stability of the interaction to find key structural characteristics that explain the antagonist activities of this set of ligands...
October 18, 2018: Journal of Molecular Graphics & Modelling
Yongxin Xu, Minjie Li, Yan Fu, Tian Lu, Yanni Hu, Wencong Lu
Dye-sensitized solar cells (DSSCs) are currently the most widely developed low-cost photovoltaic devices. A series of D-A-π-A metal-free organic dyes based on IQ1 were designed and theoretically characterized by introducing different auxiliary acceptors. The results show that the introduction of auxiliary heterocyclic acceptors could effectively tune the photoelectronic properties. In addition, all designed dyes exhibit better optoelectronic properties than IQ1. In particular, dye PIAQ not only has excellent light harvesting capability over the entire visible region and a portion of the near-infrared region, wider light harvesting efficiency (LHE) curve and larger maximum short-circuit current density (JSC max ), but also has narrower energy gap (HOMO-LUMO), larger shift of the conduction band energy level (ΔECB ) and lower injection and regeneration driving force...
October 16, 2018: Journal of Molecular Graphics & Modelling
Guedmiller S Oliveira, Jéssica C M Ierich, Ariana S Moraes, Gisela B R F Silva, Yanyun Liu, Lourival R de S Neto, Roberto R Faria, Eduardo F Franca, Luiz C G Freitas, James M Briggs, Fabio L Leite
Experimental results for the antibody known as immunoglobulin G - IgG interacting with phenobarbital were obtained via atomic force microscopy (AFM) and thereafter investigated using computer simulation modeling tools. Using molecular dynamics simulation and docking calculations, the energetically stable configurations of an immobilized antibody over a silicon surface were searched. Six stable configurations of the immobilized antibody over the silicon nitride surface covered by linker molecules were found...
October 13, 2018: Journal of Molecular Graphics & Modelling
Jialing Ma, Hui Zhang, Xin Zhang, Ming Lei
Combination of dopamine D3 antagonism and serotonin 5-HT1A agonism leads to an effective way to atypical antipsychotics. In this work, two predictive 3D-QSAR models were bulit for D3 R antagonists and 5-HT1A R agonists, respectively. Based on the steric and electrostatic information of contour maps, four compounds with improved predicted activities were newly designed. In addition, molecular docking and ADMET properties suggested that designed molecules had strong interactions with receptors and low hepatotoxicity...
October 12, 2018: Journal of Molecular Graphics & Modelling
Vinícius Gonçalves Maltarollo, Marina Ferrara de Resende, Thales Kronenberger, Cleudiomar Inácio Lino, Maria Clara Pinheiro Duarte Sampaio, Maira Galdino da Rocha Pitta, Moacyr Jesus Barreto de Melo Rêgo, Renata Adriana Labanca, Renata Barbosa de Oliveira
The antioxidant potential of a series of thiazolylhydrazone derivatives was investigated using three different methods namely DPPH, ABTS and FRAP assays. In general, the tested compounds showed higher or comparable activity to that of curcumin, used as positive control. Chemometric analyses demonstrated that the presence of hydrazone moiety is required for the activity of this class of compounds. From these results, compound 4 was identified as the most promising molecule and was then selected for further studies...
October 12, 2018: Journal of Molecular Graphics & Modelling
Ezgi Gulcay, Ilknur Erucar
Covalent organic frameworks (COFs), metal organic frameworks (MOFs) and zeolitic imidazolate frameworks (ZIFs) have been widely studied in gas separation applications due to their large surface areas, high pore volumes, tunable pore sizes and chemical stabilities. In this study, separation performances of 153 COFs, 14 IRMOFs and 8 ZIFs were assessed for efficient removal of carbon tetrachloride (CCl4 ) from CCl4 /Ar, CCl4 /N2 , CCl4 /O2 mixtures at 298 K and infinite dilution. The top performing three materials in each group, namely, borazine-linked polymer (BLP-2H-AA), IRMOF-11 and ZIF-6 were identified...
October 11, 2018: Journal of Molecular Graphics & Modelling
Sergey Trepalin, Sasha Gurke, Mikhail Akhukov, Andrey Knizhnik, Boris Potapkin
Novel logarithmic time algorithm is proposed for determining the order of chemical bonds from known valences of the atoms. The algorithm has the order of complexity N · log(N) and is applicable to polycyclic compounds containing a combination of the cycles of any size and the atoms with the valences ≤4 in cycle nodes. The algorithm is applicable to structures containing triple and cumulene bonds in the cycles. It was tested for graphene, C[12,12] nanotubes, graphyne-GY1, graphyne-GY7, graphyne-like nanotube, fullerenes C20, C60, C70, C80, C82 and their aza-analogs, polypentadienes, as well as for porphine...
October 11, 2018: Journal of Molecular Graphics & Modelling
Chao Ma, Baichun Hu, Linkui Zhang, Ying Zhao, Mingxing Wang, Jian Wang, Maosheng Cheng
The interaction of GluN2B-Containing NMDA Receptor with 18 antagonists were investigated by a combined ligand-based and target-based approach. First, two distinct pharmacophore models were generated for antagonists which cluster in two groups with Catalyst (HipHop module). The pharmacophore of "ifenprodil group" antagonists includes three hydrophobic groups, one H-bond donor and one H-bond acceptor, the pharmacophore of "EVT101 group" antagonists involves one aromatic ring, two hydrophobic groups and one H-bond acceptor...
October 10, 2018: Journal of Molecular Graphics & Modelling
Ishfaq A Sheikh, Essam H Jiffri, Ghulam Md Ashraf, Mohammad A Kamal
Lactoperoxodase (LPO) is a heme peroxidase enzyme present in mammalian milk. It is an antimicrobial protein with wide range of industrial applications. Although the three dimensional structure of LPO from various mammalian species has been reported, but its structure from camel source is still unknown. So far, the crystallization attempts have not been successful in determining camel LPO (cLPO) structure. Herein, we developed the three dimensional structure of cLPO by homology modeling approach using prime module available in Schrodinger suite...
October 10, 2018: Journal of Molecular Graphics & Modelling
Navanath M Kumbhar, Janhavi S Gopal
A quantum chemical semi-empirical RM1 approach was used to deduce the structural role of hypermodified nucleoside 5-carboxymethylaminomethyluridine 5'-monophosphate (pcmnm5 U) from 'wobble' (34th) position of mitochondrial tRNAs. The energetically preferred pcmnm5 U(34) adopted a 'skew' conformation for C5-substituted side chain (-CH2 -NH2 + -CH2 -COO- ) moiety that orient towards the 5'-ribose-phosphate backbone, which support 'anti' orientation of glycosyl (χ34 ) torsion angle. Preferred conformation of pcmnm5 U(34) was stabilized by O(4) … HC(10), O1P⋯HN(11), O(15) … HN(11), O(15) … HC(10), O4' … HC(6) and O(2) … HC2' hydrogen bonding interactions...
October 9, 2018: Journal of Molecular Graphics & Modelling
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