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Journal of Molecular Graphics & Modelling

Urszula Uciechowska-Kaczmarzyk, Isaure Chauvot de Beauchene, Sergey A Samsonov
We present a benchmarking study for protein-glycosaminoglycan systems with eight docking programs: Dock, rDock, ClusPro, PLANTS, HADDOCK, Hex, SwissDock and ATTRACT. We used a non-redundant representative dataset of 28 protein-glycosaminoglycan complexes with experimentally available structures, where a glycosaminoglycan ligand was longer than a trimer. Overall, the ligand binding poses could be correctly predicted in many cases by the tested docking programs, however the ranks of the docking poses are often poorly assigned...
April 2, 2019: Journal of Molecular Graphics & Modelling
Sanjib Paul, Tanmoy Kumar Paul, Srabani Taraphder
The choice of suitable collective variables in formulating an optimal reaction coordinate is a challenging task for activated transitions between a pair of stable states especially when dealing with biochemical changes such as enzyme catalyzed reactions. A detailed benchmarking study is carried out on the choice of collective variables that can distinguish between the stable states unambiguously. We specifically address the issue if these variables may be directly used to model the optimal reaction coordinate, or if it would be better to use their orthogonalized counterparts...
March 30, 2019: Journal of Molecular Graphics & Modelling
Song Hu, Yawen Dong, Xiao Zhao, Li Zhang
OfHex1 is a potential target for the rational design of pesticides. TMG-chitotriomycin is one of the most highly specific known inhibitors of chitinolytic β-GlcNAcases from bacteria, fungi and insects. TMG-chitotriomycin and its analogues show different activities to OfHex1, dependent on the number of GlcNAc units. Subsequently, it is essential to explore how these GlcNAc unit number changes cause alterations in activity. In this study, we examined the free energy patterns and per residue decomposition of binding within the complexes of OfHex1 and a series of inhibitors, utilizing restricted molecular dynamics (MD) and water-mediated MM/GBSA calculations...
March 27, 2019: Journal of Molecular Graphics & Modelling
Christopher Llynard D Ortiz, Hosea D Matel, Ricky B Nellas
Drawbacks of industrially-used fructosyltransferases (FTs) such as low optimum temperature and low fructooligosaccharides (FOS) yield necessitates the search for engineered FTs that are highly thermostable and active. With the availability of the first plant FT crystal structure from Pachysandra terminalis (PDB ID: 3UGH), computer-aided protein engineering of plant FT is now feasible. To obtain insights on the effect of specific mutations i.e. disulfide bridge introduction, wild-type and mutant FTs were subjected to a 15 μs Martini Coarse-grained Molecular Dynamics (CGMD) simulations at 303 K and 334 K...
March 24, 2019: Journal of Molecular Graphics & Modelling
Pourseyed Aghaei Fatematossadat, Mahnaz Mohammadi, S Ehsan Roozmeh
In this paper, we study magnetic and structural properties of silver and gold-coated iron nanoparticle as novel drug delivery systems for the two commercially famous cancer treatment drugs, using the density functional theory (DFT) computations. Our calculations show that silver and gold-coated iron nanoparticle have magnetization and the magnetic moment of the Fe atom in the Fe@(Ag/Au)n core-shells saturated to a value of about 3 μB . Thus the Fe@(Ag/Au)n core-shells are very promising to be functionalized for targeted drug delivery...
March 21, 2019: Journal of Molecular Graphics & Modelling
Jiu-Yu Zhan, Jie Ma, Qing-Chuan Zheng
Asciminib, a highly selective non-ATP competitive inhibitor of BCR-ABL, has demonstrated to be a promising drug for patients with chronic myeloid leukemia. It is a pity that two resistant mutations (I502L and V468F) have been found during the clinical trial, which is a challenge for the curative effect of Asciminib. In this study, molecular dynamics simulations and molecular mechanics generalized Born surface area (MM-GB/SA) calculations were performed to investigate the molecular mechanism of Asciminib resistance induced by the two mutants...
March 21, 2019: Journal of Molecular Graphics & Modelling
Azeemullah A Syed, Kalkooru L Venkatraman, Alka Mehta
Thrombosis represents a major cause of morbidity and mortality around the world. Peptides isolated from natural sources have been proven to have anticoagulant and antithrombotic properties. VITPOR AI, a 16-mer peptide, isolated from Porphyra yezoensis was reported to have anticoagulant property. In this study, the coagulation factor XIIa activity in the presence of VITPOR AI was determined. Molecular modelling was performed to investigate the interaction between peptide and FXIIa. The structure of the peptide was predicted using PEP-FOLD3 server and simulated by molecular dynamics (MD) using GROMACS package...
March 21, 2019: Journal of Molecular Graphics & Modelling
Oleh H Havrysh, Vladyslav Kholodovych, Evgen A Andreev
An application of contiguous filling of space with convex polyhedra, also known as Frank-Kasper (FK) atomic domains is demonstrated here for modeling of atomic molecular structures. Both regular, when all polyhedron edges have equal length, and strained, depending on the topology of the polyhedron the length of its edges may slightly fluctuate from the common length, polyhedra are used. Polyhedra are connected to each other in agreement with Plateau's laws to form a contiguous uninterrupted space. An application of a new approach is demonstrated for a modeling of structures of graphite, graphene, graphane, diamond and two types of ice...
March 18, 2019: Journal of Molecular Graphics & Modelling
Naveed Khan, Sobia Ahsan Halim, Waqasuddin Khan, Syed Kashif Zafar, Zaheer Ul-Haq
Obesity is the fifth primary hazard for mortality in the world; hence different therapeutic targets are explored to overcome this problem. Endocannabinoid is identified as the emerging target for the treatment of obesity as Cannabinoid 1 (CB1) receptor over-activation resulted in abdominal obesity. Potent antagonists or inverse agonists for CB1 receptor are the new strategies to develop anti-obesity drugs. Here, ligand-based 3D-QSAR studies was performed on 100 analogues belonging to a class of 1,2,4-tirazole containing diarylpyrazolylcarboxamide as CB1 receptor antagonists...
March 17, 2019: Journal of Molecular Graphics & Modelling
Ivan Ilin, Elena Lipets, Alexey Sulimov, Danil Kutov, Khidmet Shikhaliev, Andrey Potapov, Michael Krysin, Fedor Zubkov, Lyudmila Sapronova, Fazoyl Ataullakhanov, Vladimir Sulimov
Factor Xa is a serine protease representing a crucial element in the coagulation process and an attractive target for anticoagulant therapy. At the present time there are several chemical classes of factor Xa inhibitors with proven activity. Furthermore, three factor Xa inhibitors have been approved for the medical use to date. However, therapy with these medications is accompanied by substantial adverse effects. In this background, the structure-based computational approach combining molecular docking and semiempirical quantum chemical calculations was applied for a search for new effective factor Xa inhibitors...
March 16, 2019: Journal of Molecular Graphics & Modelling
Ming Yang, Jianghe Luo, Zhumei Zeng, Ling Yang, Limian Xu, Yan Li
Oxytocin plays a vital role in the occurrence of preterm birth by interacting with oxytocin receptor (OTR), and thus OTR antagonists provide effective approaches for the treatment of early birth. Presently, for purpose of exploring the structural traits affecting the antagonism potency, the up-to-date largest set of 121 2,5-diketopiperazine derivatives as OTR antagonists was subjected to ligand-based three-dimensional quantitative structure-activity (3D-QSAR) analysis applying comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods...
March 16, 2019: Journal of Molecular Graphics & Modelling
Yung-Ting Lee, Taisuke Ozaki
The OpenMX Viewer (Open source package for Material eXplorer Viewer) is a web-based graphical user interface (GUI) program for visualization and analysis of crystalline and molecular structures and 3D grid data in the Gaussian cube format such as electron density and molecular orbitals. The web-based GUI program enables us to quickly visualize crystalline and molecular structures by dragging and dropping XYZ, CIF, or OpenMX input/output files, and analyze static/dynamic structural properties conveniently in a web browser...
March 15, 2019: Journal of Molecular Graphics & Modelling
Eduardo R Almeida, Leonardo A De Souza, Wagner B De Almeida, Hélio F Dos Santos
The medication with Pt-based antitumor drug cisplatin has demonstrated effective results against cancer cells, despite the severe side effects due to the high toxicity associated with the low selectivity of these anticancer agents. An alternative to overcome or decrease the side effects is to use drug delivery systems, which can carry high doses of the anticancer drug and promote its slow and targeted release to the tumor sites. Herein, we used molecular dynamics to study prototypes of the complexes formed by the encapsulated cisplatin and carbon nanohorns (CNH), with the purpose to characterize its structures and dynamical behavior in aqueous solution, an important feature to assess the potentiality of using CNH as carrier systems...
March 15, 2019: Journal of Molecular Graphics & Modelling
Laura J Kingsley, Vincent Brunet, Gerald Lelais, Steve McCloskey, Kelly Milliken, Edgardo Leija, Stephen R Fuhs, Kai Wang, Edward Zhou, Glen Spraggon
In drug discovery, structural knowledge of a target enables structure-based design approaches and thereby reduces the time and labor required to develop a therapy. Whilst molecular graphics frameworks coupled with computational analysis are now ubiquitous tools for the structural and computational biologist, sharing the detailed visualization and derived structural information with non-expert users still presents a challenge. Here we describe an intuitive virtual world for viewing, manipulating, and modifying chemical and macromolecular structures in a fully immersive and collaborative 3D environment...
March 12, 2019: Journal of Molecular Graphics & Modelling
Walid Taouali, Mark E Casida, Sami Znaidia, Kamel Alimi
In this work, we focus on designing a donor copolymer for the improvement of photovoltaic performance. Using density functional theory and time-dependent density functional theory, we investigated the electronic, optical and charge transfer properties of a series of new designed copolymers based on the reported copolymer Pa0 which is composed of a donor fluorene unit and an acceptor 4,7-dithien-2-yl-2,1,3-benzothiadiazole. We first obtained two copolymers Pb0 and Pc0 by replacing the benzothiadiazole (BTZ) with two different strong acceptors units to decrease the LUMO level of conjugated polymers...
March 12, 2019: Journal of Molecular Graphics & Modelling
Lei Zhang, Shuai Lin, Bo Wu, Qingfang Li, Jingfa Li
Two-dimensional black phosphorus (phosphorene) has drawn much attention in recent years due to its excellent electronic and optical properties. In this manuscript, we employ ab initio calculations to investigate the structural origin of the phosphorene/perovskite heterostructure. The calculations suggest that the chemical stability and the mechanical stability depend on the surface terminations, and the mechanical stability of the phosphorene/perovskite heterojunction should be further improved. The weak interactions between the P atoms in the phosphorene and the under-coordinated Pb atoms at the perovskite surfaces, as well as the weak interfacial charge transfer characters, are proposed to be mainly responsible for the moderate heterostructure stability...
March 12, 2019: Journal of Molecular Graphics & Modelling
Shin-Ichiro Ozawa, Miki Takahashi, Noriyuki Yamaotsu, Shuichi Hirono
The term chymase refers to a family of chymotrypsin-like serine proteases stored within the secretory granules of mast cells. Recently, a variety of small molecule inhibitors for chymase have been developed with a primary focus on the treatment of cardiovascular diseases. Despite the expected therapeutic benefit of these chymase inhibitors, they have not been used clinically. Here, we attempted to identify new chymase inhibitors using a multistep structure-based virtual screening protocol combined with our knowledge-based in silico fragment mapping technique...
March 12, 2019: Journal of Molecular Graphics & Modelling
Haralambos Tzoupis, Agathi Nteli, Jamie Platts, Efi Mantzourani, Theodore Tselios
Sexual maturation of human cells in ovaries and prostate is linked to the biochemical cascade initiated by the activation of cell receptors through the binding of Gonadotropin Releasing Hormone (GnRH). The GnRH receptors (GnRHR) are part of the rhodopsin G-protein coupled receptor (GPCR) family and consist of seven trans-membrane helical domains connected via extra- and intra-cellular segments. The GnRH-GnRHR complex has been implicated in various forms of prostate and ovarian cancer. The lack of any structural data about the GnRH receptor impedes the design of antagonists for use in cancer treatment...
March 11, 2019: Journal of Molecular Graphics & Modelling
Jirayu Kammarabutr, Panupong Mahalapbutr, Bodee Nutho, Nawee Kungwan, Thanyada Rungrotmongkol
Hepatitis C has become an important health problem that requires expensive treatment and leads to liver tumorigenesis. Hepatitis C virus (HCV), which is the main cause of hepatitis C, has a high mutation rate due to the lack of proofreading activity of the RNA polymerase enzyme. The NS3/4A serine protease is an important target for anti-HCV drug discovery and development because of its crucial role in the cleavage of the polypeptides involved in viral replication. In the present study, all-atom molecular dynamics simulation was performed to elucidate the effect of the single point mutations R155K and D168A in the HCV genotype 1 NS3/4A protease on the structural dynamics, molecular interactions and susceptibility of asunaprevir (ASV), a second-generation NS3/4A protease inhibitor...
March 11, 2019: Journal of Molecular Graphics & Modelling
Sergey V Bondarchuk
The mechanism of the compression-induced decomposition of aryl diazonium chlorides is proposed on the basis of quantum-chemical calculations of both the isolated cations and crystalline materials. The electron transfer from the anion to the cation, followed by the crystal decomposition, is observed with the rise of pressure. Taking the known nature of the structural changes in cations undergone upon reduction, five structural, vibrational and electronic determinants of impact sensitivity are found. Thus, a correlation (R2  = 0...
March 11, 2019: Journal of Molecular Graphics & Modelling
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