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Journal of Molecular Graphics & Modelling

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https://www.readbyqxmd.com/read/28641211/specific-interactions-between-androgen-receptor-and-its-ligand-ab-initio-molecular-orbital-calculations-in-water
#1
Ittetsu Kobayashi, Ryosuke Takeda, Rie Suzuki, Kanako Shimamura, Hiromi Ishimura, Ryushi Kadoya, Kentaro Kawai, Midori Takimoto-Kamimura, Noriyuki Kurita
The Androgen Receptor (AR) is a family of nuclear receptor proteins and a ligand-activated transcription factor. Since its abnormal activation can cause the progression of prostate cancer, numerous types of antagonists against AR have been developed as promising agents for treating prostate cancers. We here investigated the specific interactions between AR and several types of non-steroid agents at an electronic level, using ab initio molecular simulations based on molecular mechanics and ab initio fragment molecular orbital (FMO) methods From the results obtained by FMO, we proposed novel agents as potent ligands against AR and investigated the binding properties between AR and these agents to confirm that some of them can bind more strongly with AR than the existing non-steroid agents and can be strongly effective ligands against AR...
June 13, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28641209/adsorption-of-no2-molecules-on-armchair-phosphorene-nanosheet-for-nano-sensor-applications-a-first-principles-study
#2
V Nagarajan, R Chandiramouli
The electronic and NO2 adsorption properties of hydrogenated armchair phosphorene nanosheet device is investigated through density functional theory (DFT) and non-equilibrium Green's function method (NEGF). The armchair phosphorene nanosheet is used for the detection of NO2 gas in phosphorene molecular device. The DOS spectrum demonstrates the change in peak maxima due to transfer of electrons between NO2 gas and phosphorene base material. The change in the peak amplitude is observed along the valance band as well as in the conduction band in the transmission spectrum of phosphorene device...
June 13, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28628859/structural-and-functional-effects-of-nucleotide-variation-on-the-human-tb-drug-metabolizing-enzyme-arylamine-n-acetyltransferase-1
#3
Ruben Cloete, Wisdom A Akurugu, Cedric J Werely, Paul D van Helden, Alan Christoffels
The human arylamine N-acetyltransferase 1 (NAT1) enzyme plays a vital role in determining the duration of action of amine-containing drugs such as para-aminobenzoic acid (PABA) by influencing the balance between detoxification and metabolic activation of these drugs. Recently, four novel single nucleotide polymorphisms (SNPs) were identified within a South African mixed ancestry population. Modeling the effects of these SNPs within the structural protein was done to assess possible structure and function changes in the enzyme...
June 10, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28645089/drug-resistance-mechanism-of-l10f-l10f-n88s-and-l90m-mutations-in-crf01_ae-hiv-1-protease-molecular-dynamics-simulations-and-binding-free-energy-calculations
#4
C S Vasavi, Ramasamy Tamizhselvi, Punnagai Munusami
HIV-1 protease plays a crucial role in viral replication and maturation, which makes it one of the most attractive targets for anti-retroviral therapy. The majority of HIV infections in developing countries are due to non-B subtype. Subtype AE is spreading rapidly and infecting huge population worldwide. The mutations in the active site of subtype AE directly impair the interactions with the inhibitor. The non-active site mutations influence the binding of the inhibitor indirectly and their resistance mechanism is not well understood...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28641210/comparative-analysis-of-polyspecificity-of-the-endogenous-trna-synthetase-of-different-expression-host-towards-photocrosslinking-amino-acids-using-an-in-silico-approach
#5
Nadarajan Saravanan Prabhu, Hyungdon Yun
Photo-induced covalent crosslinking has emerged as the powerful strategy for analyzing and characterizing the protein-protein interaction and mapping protein 3D conformations. In the last decades, a number of photocrosslinking amino acids have been reported but only a few have been efficiently utilized for photocrosslinking purposes. Recently, incorporation of diazirine containing photoactivatable analogs such as photo-methionine, photo-leucine, photo-isoleucine and photo-lysine into target proteins were accomplished in live cells (Human A549cells, HEK 293) by depleting corresponding natural amino acid and supplementing these analogs in the medium...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28628858/unravelling-the-structural-interactions-between-pkr-kinase-domain-and-its-small-molecule-inhibitors-using-computational-approaches
#6
Sagar Barage, Abhijeet Kulkarni, Jayanta K Pal, Manali Joshi
The RNA-dependent protein kinase (PKR), an eIF2α kinase plays an important role in anti-viral response, apoptosis and cell survival. It is also implicated to play a role in several cancers, metabolic and neurodegenerative disorders. A few ATP competitive inhibitors of the PKR have been reported in the literature with promising results in vitro and in vivo. The aim of this study was to unravel the structural interactions between these inhibitors and the PKR kinase domain using molecular simulations and docking...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28628857/identification-of-b-and-t-cell-epitope-based-peptide-vaccine-from-igf-1-receptor-in-breast-cancer
#7
Manijeh Mahdavi, Violaine Moreau, Majid Kheirollahi
The insulin-like growth factor-1 receptor (IGF-1R) plays a key role in proliferation, growth, differentiation, and development of several human malignancies including breast and pancreatic adenocarcinoma. IGF-1R targeted immunotherapeutic approaches are particularly attractive, as they may potentially elicit even stronger antitumor responses than traditional targeted approaches. Cancer peptide vaccines can produce immunologic responses against cancer cells by triggering helper T cell (Th) or cytotoxic T cells (CTL) in association with Major Histocompatibility Complex (MHC) class I or II molecules on the cell surface of antigen presenting cells...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28623781/inhibition-activities-of-catechol-diether-based-non-nucleoside-inhibitors-against-the-hiv-reverse-transcriptase-variants-insights-from-molecular-docking-and-oniom-calculations
#8
Pabitra Narayan Samanta, Kalyan Kumar Das
The therapeutic effectiveness of the catechol diether analogs against both the wild-type and drug-resistant reverse transcriptase (RT) mutants of HIV strains are investigated by performing molecular docking and hybrid ONIOM calculations. The docking protocol has been used to predict the binding modes of the non-nucleoside inhibitors inside the active site cavity of the viral enzymes. For each enzyme-inhibitor adduct, the predicted docked poses are assessed by employing different scoring function based programs...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28622610/f1174v-mutation-alters-the-alk-active-conformation-in-response-to-crizotinib-in-nsclc-insight-from-molecular-simulations
#9
Fariba Dehghanian, Maryam Kay, Sadeq Vallian
Crizotinib is an efficient antineoplastic drug for treatment of non-small cell lung carcinoma (NSCLC), which is identified as an anaplastic lymphoma kinase (ALK) inhibitor. F1174V is a recently identified acquired point mutation relating to the Crizotinib resistance in NSCLC patients. The mechanism of Crizotinib resistance relating to F1174V mutation as a non-active site mutation remains unclear. In this study, the molecular dynamic simulation was used to investigate the possible mechanisms by which F1174V mutation may affect the structure and activity of ALK kinase domain...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28618335/specific-interactions-between-zinc-metalloproteinase-and-its-inhibitors-ab-initio-fragment-molecular-orbital-calculations
#10
Ayami Ara, Ryushi Kadoya, Hiromi Ishimura, Kanako Shimamura, Ingebrigt Sylte, Noriyuki Kurita
Bacteria secrete the enzyme pseudolysin (PLN) to degrade exocellular proteins, and the produced peptides are used as a nutrient for the bacteria. It is thus expected that inhibition of PLN can suppress bacterial growth. Since such inhibitors do not attack to bacteria directly, the risk of producing drug-resistance bacteria is less. However, endogenous proteinases such as the matrix metalloproteinases (MMPs) have active site similar to that of PLN, and there is a possibility that PLN inhibitors also inhibit the activity of MMPs, resulting in a loss of substrate degradation by these proteinases...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28618334/comprehensive-modelling-and-simulation-of-cylindrical-nanoparticles-manipulation-by-using-a-virtual-reality-environment
#11
Moharam Habibnejad Korayem, Ali Kafash Hoshiar, Maedeh Ghofrani
With the expansion of nanotechnology, robots based on atomic force microscope (AFM) have been widely used as effective tools for displacing nanoparticles and constructing nanostructures. One of the most limiting factors in AFM-based manipulation procedures is the inability of simultaneously observing the controlled pushing and displacing of nanoparticles while performing the operation. To deal with this limitation, a virtual reality environment has been used in this paper for observing the manipulation operation...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28628860/in-silico-modeling-on-adme-properties-of-natural-products-classification-models-for-blood-brain-barrier-permeability-its-application-to-traditional-chinese-medicine-and-in-vitro-experimental-validation
#12
Xiuqing Zhang, Ting Liu, Xiaohui Fan, Ni Ai
In silico modeling of blood-brain barrier (BBB) permeability plays an important role in early discovery of central nervous system (CNS) drugs due to its high-throughput and cost-effectiveness. Natural products (NP) have demonstrated considerable therapeutic efficacy against several CNS diseases. However, BBB permeation property of NP is scarcely evaluated both experimentally and computationally. It is well accepted that significant difference in chemical spaces exists between NP and synthetic drugs, which calls into doubt on suitability of available synthetic chemical based BBB permeability models for the evaluation of NP...
June 7, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28600973/understanding-the-molecular-basis-of-stability-in-kunitz-sti-family-of-inhibitors-in-terms-of-a-conserved-core-tryptophan-residue-a-theoretical-investigation
#13
Ravi Datta Sharma, Nabajyoti Goswami, Debasree Ghosh, Sudip Majumder
β-trefoil is one of the superfolds among proteins. Important classes of proteins like Interleukins (ILs), FibroblastGrowth Factors (FGFs), Kunitz (STI) family of inhibitors etc. belong to this fold. Kunitz (STI) family of inhibitors of proteins possess a highly conserved and structurally important Trytophan 91 (W91) residue, which stitches the top layer of the barrel with the lid. In this article we have investigated the molecular insights of the involvement of this W91 residue in the stability and folding pathway of Kunitz (STI) family...
June 3, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28651183/investigating-the-effect-of-different-transducer-stiffness-values-on-the-contactin-complex-detachment-by-steered-molecular-dynamics
#14
Parnian Kianfar, Nabiollah Abolfathi, Navid Zarif Karimi
This study investigated the adhesion behavior of Contactin4 (CNTN4), a member of Immunoglobulin Super Family (Ig-SF) of cell adhesion molecules. Contactin4 plays a crucial role in the formation, maintenance, and plasticity of neuronal networks. Contactin in its complex configuration with protein tyrosine phosphatase gamma (PTPRG) was selected for simulation. By utilizing Steered Molecular Dynamics (SMD), the uniaxial force was applied to induce unbinding of the complex, and the force-induced detachment of complex components was probed...
June 2, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28609757/a-molecular-docking-study-of-the-interactions-between-human-transferrin-and-seven-metallocene-dichlorides
#15
Jorge R Güette-Fernández, Enrique Meléndez, Wilson Maldonado-Rojas, Carlos Ortega-Zúñiga, Jesus Olivero-Verbel, Elsie I Parés-Matos
Human Transferrin (hTf) is a metal-binding protein found in blood plasma and is well known for its role in iron delivery. With only a 30% of its capacity for Fe(+3) binding, this protein has the potential ability to transport other metal ions or organometallic compounds from the blood stream to all cell tissues. In this perspective, recent studies have described seven metallocene dichlorides (Cp2M(IV)Cl2, M(IV)=V, Mo, W, Nb, Ti, Zr, Hf) suitable as anticancer drugs and less secondary effects than cisplatin...
May 30, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28651184/computational-study-of-structural-optoelectronic-and-nonlinear-optical-properties-of-dynamic-solid-state-chalcone-derivatives
#16
Aijaz Rasool Chaudhry, Ahmad Irfan, Shabbir Muhammad, Abdullah G Al-Sehemi, R Ahmed, Zhang Jingping
In the present study, we use the state of art density functional theory (DFT) techniques to calculate the structural, optoelectronic and nonlinear optical (NLO) properties for two novel chalcone derivatives. The geometrical structures of chalcone derivatives compound 1 and 2 are optimized using periodic boundary conditions (PBC) in solid-state phase as well as isolated single molecular geometry in the gas phase. The reasonable agreement is found among experimental, solid-state and gas phase single molecular geometries, which provide us, further confidence to explore the potential of above-entitled derivatives as good functional materials for electro-optical applications...
May 29, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28586703/exploring-the-potential-of-boron-doped-nanographene-as-efficient-charge-transport-and-nonlinear-optical-material-a-first-principles-study
#17
Ahmad Irfan, Aijaz Rasool Chaudhry, Shabbir Muhammad, Abdullah G Al-Sehemi
Owing to their excellent electrochemical properties, graphenes found applications in several fields ranging from semiconductors, solar cells, field effect transistors, and nanoscale electronic devices as well as in nonlinear optical (NLO) applications. The structural features, electro-optical, charge transport and nonlinear optical properties of the boron-doped graphene (BG) compound 1 were studied using density functional theory methods The BG compound comprises a central electron deficient site of boron atoms, which can serve as electron acceptor while terminal alkoxy groups as donors leading to powerful donor-π-acceptor (D-π-A) configuration...
May 26, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28586702/first-principle-electron-transport-modeling-of-be-doped-organic-molecular-junctions
#18
Rupan Preet Kaur, Ravinder Singh Sawhney, Derick Engles
The transport properties of beryllium doped anthracene molecular junction are investigated using density functional non-equillibrium Green's function method. The equilibrium conductance of anthracene Metal-molecule-Metal (MmM) junction increases by approximately 77% by adding beryllium impurity to it. The electronic transport characteristics under both zero bias as well as finite bias are explored of such molecular junction. We observe novel attributes such as molecular rectification and NDR behavior for the molecular junction under consideration...
May 26, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28582696/structural-basis-for-the-potent-inhibition-of-the-hiv-integrase-ledgf-p75-protein-protein-interaction
#19
Sergio R Ribone, Mario A Quevedo
Integrase (IN) constitutes one of the key enzymes involved in the lifecycle of the Human Immunodeficiency Virus (HIV), the etiological agent of AIDS. The biological role of IN strongly depends on the recognition and binding of cellular cofactors belonging to the infected host cell. Thus, the inhibition of the protein-protein interaction (PPI) between IN and cellular cofactors has been envisioned as a promising therapeutic target. In the present work we explore a structure-activity relationship for a set of 14 compounds reported as inhibitors of the PPI between IN and the lens epithelium-derived growth factor (LEDGF/p75)...
May 26, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28582695/identification-of-potent-inhibitors-of-dna-methyltransferase-1-dnmt1-through-a-pharmacophore-based-virtual-screening-approach
#20
Shagun Krishna, Samriddhi Shukla, Amar Deep Lakra, Syed Musthapa Meeran, Mohammad Imran Siddiqi
DNA methylation is an epigenetic change that results in the addition of a methyl group at the carbon-5 position of cytosine residues. DNA methyltransferase (DNMT) inhibitors can suppress tumour growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. Additionally, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects. In the present study, we have designed a workflow by integrating various ligand-based and structure-based approaches to discover new agents active against DNMT1...
May 25, 2017: Journal of Molecular Graphics & Modelling
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