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https://www.readbyqxmd.com/read/30099452/11%C3%AE-hydroxysteroid-dehydrogenase-type-1-inhibitor-development-by-lentiviral-screening-based-on-computational-modeling
#1
Haifeng Liu, Lingyu Li, Chunlei Zhang, Hongzhi Li, Jieting Liu, Chunyin Tang, Yufei Zhang, Dan Wu, Yanhui Chu, Yan Wu, Xiaohuan Yuan
In this study, rat and human 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) have been cloned by lentiviral transduction and expressed by CHO-K1 cells. The results showed that recombinant plasmids contained R11bhsd1 or H11bhsd1 have been constructed, which is consistent with the gene bank respectively. A clone cell was selected with G418 and cultivated to express 11β-HSD1. 11β-HSD1 catalytic activity of rat and human were 99.5 and 98.7%, respectively, determined by scanning radiometer. And the cloned CHO-K1 cells expressed the protein of 11β-HSD1 in a long-term and stable manner, which makes it suitable for screening 11β-HSD1 inhibitor...
August 10, 2018: Pharmacology
https://www.readbyqxmd.com/read/30096627/rational-in-silico-design-of-novel-%C3%AE-glucosidase-inhibitory-peptides-and-in-vitro-evaluation-of-promising-candidates
#2
Mohammed Auwal Ibrahim, Megan J Bester, Albert W Neitz, Anabella R M Gaspar
Treatment of type 2 diabetes is achieved through the inhibition of carbohydrate hydrolyzing enzymes such as α-glucosidase and α-amylase. The present study was conducted to identify novel α-glucosidase inhibitory peptides and to validate the α-glucosidase and α-amylase inhibitory activities of two promising candidates. A total of 4210 potential α-glucosidase inhibitory peptides with 3-5 amino acid residues were designed and individually subjected to in silico simulated gastrointestinal (GIT) digestion using the BIOPEP database...
August 7, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/30086194/in-vitro-inhibition-potential-of-mono-n-octyl-phthalate-on-mycobacterium-tuberculosis-h37ra-possibility-of-binding-to-mycobacterial-pknb-an-in-silico-approach
#3
Muniyan Rajiniraja, Akella Sivaramakrishna, Varatharajan Sabareesh, Gurunathan Jayaraman
Fatty acids, of specific chain lengths, have been shown to inhibit the growth of Mycobacterium tuberculosis. In the present study, specific synthetic aromatic derivatives of n-octyl esters were investigated for their property to inhibit the growth of Mycobacterium tuberculosis H37Ra. Agar well diffusion assay indicated that the crude synthetic derivatives obtained by the esterification of phthalic acid and n-octanol exhibited antimycobacterial activity. Further, the activity was authenticate with the miroplate alamar blue assay (MABA)...
August 7, 2018: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/30072177/role-of-steroid-therapy-after-ischemic-stroke-by-n-methyl-d-aspartate-receptor-gene-regulation
#4
Abolfazl Azami Tameh, Mohammad Karimian, Zahra Zare-Dehghanani, Younes Aftabi, Cordian Beyer
BACKGROUND: Stroke is the main cause of cerebrovascular disease mortality. Prolonged stimulation of n-methyl-d-aspartate (NMDA) receptor subtypes by the accumulation of glutamate neurotransmitter in the extracellular space after a stroke could activate cell death pathways. It is reported that progesterone provides different mechanisms of neuroprotection and could be considered as a candidate for stroke treatment. This study aimed to investigate progesterone impact on the expression of NMDA receptor subunits NR1, NR2 (A and B), NR3 (A and B) after an experimental model of ischemic stroke which is followed by an in silico analysis...
July 30, 2018: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/30066129/structure-based-virtual-screening-of-high-affinity-atp-competitive-inhibitors-against-human-lemur-tyrosine-kinase-3-lmtk3-domain-a-novel-therapeutic-target-for-breast-cancer
#5
Himakshi Sarma, Venkata Satish Kumar Mattaparthi
Human lemur tyrosine kinase-3 (LMTK3) is an oncogenic kinase known to regulate ER-α through phosphorylation and is considered to be a novel therapeutic target for breast cancer. In this work, we have studied the ATP-binding mechanism with LMTK3 domain and also carried out virtual screening on LMTK3 to identify lead compounds using Dock blaster server. The top scored compounds obtained from Dock blaster were then narrowed down further to six lead compounds (ZINC37996511, ZINC83363046, ZINC3745998, ZINC50456700, ZINC83351792 and ZINC83364581) based on high-binding affinity and non-bonding interactions with LMTK3 using Autodock 4...
July 31, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30061529/understanding-the-positional-binding-and-substrate-interaction-of-a-highly-thermostable-gh10-xylanase-from-thermotoga-maritima-by-molecular-docking
#6
Jiangke Yang, Zhenggang Han
Glycoside hydrolase family 10 (GH10) xylanases are responsible for enzymatic cleavage of the internal glycosidic linkages of the xylan backbone, to generate xylooligosaccharides (XOS) and xyloses. The topologies of active-site cleft determine the substrate preferences and product profiles of xylanases. In this study, positional bindings and substrate interactions of TmxB, one of the most thermostable xylanases characterized from Thermotoga maritima to date, was investigated by docking simulations. XOS with backbone lengths of two to five (X2⁻X5) were docked into the active-site cleft of TmxB by AutoDock The modeled complex structures provided a series of snapshots of the interactions between XOS and TmxB...
July 30, 2018: Biomolecules
https://www.readbyqxmd.com/read/30058412/the-in-silico-identification-of-potent-anti-cancer-agents-by-targeting-the-atp-binding-site-of-the-n-domain-of-hsp90
#7
B Sepehri, M Rezaei, R Ghavami
To identify new HSP90 inhibitors, the ATP binding site of the N-domain of HSP90 was targeted by molecular docking of a library of 23,129,083 compounds (from the ZINC database) to the ATP binding site of the N-domain of HSP90. Structure-based virtual screen (SBVS) was performed using idock software on the istar web platform. Based on idock binding energies, 40 molecules were considered as HSP90 inhibitors. In the next step, the 40 molecules and the compound AT13387 (Onalespib) were docked to the XJX binding site using AutoDock Vina software...
July 2018: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/30057554/eplerenone-reverses-cardiac-fibrosis-via-the-suppression-of-tregs-by-inhibition-of-kv1-3-channel
#8
Pei-Pei Shao, Chang-Jiang Liu, Qi Xu, Bo Zhang, Shao-Hua Li, Yang Wu, Zhan Sun, Lu-Feng Cheng
Background: Fibroblast proliferation is a critical feature during heart failure development. Previous studies reported regulatory T-lymphocytes (Tregs)' protective role against myocardial fibrosis. However, notably, Tregs also secrete fibrogenic cytokine TGF-β when activated. This study aimed to clarify the intriguing link between Tregs and fibrosis, the role of Tregs Kv1.3 potassium channel (regulating T-lymphocytes activation) in the fibrosis process, and how selective aldosterone receptor antagonist Eplerenone affects Tregs and fibrosis through its action on Kv1...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/30044621/thymol-induces-conidial-apoptosis-in-aspergillus-flavus-via-stimulating-k-eruption
#9
Liang-Bin Hu, Fang-Fang Ban, Hong-Bo Li, Pan-Pan Qian, Qing-Shan Shen, Yan-Yan Zhao, Hai-Zhen Mo, Xiaohui Zhou
Aspergillus flavus is a notorious foodborne fungus, posing a significant risk to humans in the form of hepatocellular carcinoma or aspergillosis. Thymol, as a food preservative, could efficiently kill conidia of A. flavus. However, the underlying mechanisms by which thymol kills A. flavus are not completely understood. With specific fluorescent dyes, we detected several apoptotic hallmarks, including chromatin condensation, phosphatidylserine externalization, DNA damage, mitochondrial depolarization, and caspase 9 activation in conidia exposed to 200 μg/mL of thymol, indicating that thymol induced a caspase-dependent conidial apoptosis in A...
August 6, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/30023710/superior-performance-of-the-sqm-cosmo-scoring-functions-in-native-pose-recognition-of-diverse-protein-ligand-complexes-in-cognate-docking
#10
Haresh Ajani, Adam Pecina, Saltuk M Eyrilmez, Jindřich Fanfrlík, Susanta Haldar, Jan Řezáč, Pavel Hobza, Martin Lepšík
General and reliable description of structures and energetics in protein-ligand (PL) binding using the docking/scoring methodology has until now been elusive. We address this urgent deficiency of scoring functions (SFs) by the systematic development of corrected semiempirical quantum mechanical (SQM) methods, which correctly describe all types of noncovalent interactions and are fast enough to treat systems of thousands of atoms. Two most accurate SQM methods, PM6-D3H4X and SCC-DFTB3-D3H4X, are coupled with the conductor-like screening model (COSMO) implicit solvation model in so-called "SQM/COSMO" SFs and have shown unique recognition of native ligand poses in cognate docking in four challenging PL systems, including metalloprotein...
July 31, 2017: ACS Omega
https://www.readbyqxmd.com/read/30005292/identification-of-putative-drug-targets-and-annotation-of-unknown-proteins-in-tropheryma-whipplei
#11
Navaneethan Palanisamy
Tropheryma whipplei (T. whipplei) is the causative agent of Whipple's disease and blood culture-negative endocarditis. Due to the variability of symptoms, the disease is often poorly diagnosed. Treatment for this bacterial infection is often lengthy, and improper uptake of antibiotics has resulted in relapses in many patients. In the present study, using available bioinformatic tools and databases such as the Cluster Database at High Identity with Tolerance (CD-HIT), the Basic Local Alignment Search Tool for proteins (BLASTp), the Database of Essential Genes (DEG), and the DrugBank database, 13 putative drug targets were identified in T...
June 9, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29992528/convolutional-neural-network-scoring-and-minimization-in-the-d3r-2017-community-challenge
#12
Jocelyn Sunseri, Jonathan E King, Paul G Francoeur, David Ryan Koes
We assess the ability of our convolutional neural network (CNN)-based scoring functions to perform several common tasks in the domain of drug discovery. These include correctly identifying ligand poses near and far from the true binding mode when given a set of reference receptors and classifying ligands as active or inactive using structural information. We use the CNN to re-score or refine poses generated using a conventional scoring function, Autodock Vina, and compare the performance of each of these methods to using the conventional scoring function alone...
July 10, 2018: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29989806/evaluation-of-autodock-and-autodock-vina-on-the-casf-2013-benchmark
#13
Thomas Gaillard
Computer-aided protein-ligand binding predictions are a valuable help in drug discovery. Protein-ligand docking programs generally consist of two main components: a scoring function and a search algorithm. It is of interest to evaluate the intrinsic performance of scoring functions, independently of conformational exploration, to understand their strengths and weaknesses and suggest improvements. The comparative assessment of scoring functions (CASF) provides such an evaluation. Here we add the AutoDock and Vina scoring functions to the CASF-2013 benchmark...
July 25, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29985239/quetiapine-protects-the-blood-brain-barrier-in-traumatic-brain-injury
#14
Bobby Darnell Robinson, Claire Larson Isbell, Chinchusha Anasooya Shaji, Stanley Kurek, Justin L Regner, Binu Tharakan
BACKGROUND: The integrity of the blood-brain barrier (BBB) is paramount in limiting vasogenic edema following traumatic brain injury (TBI). The purpose of this study was to ascertain if quetiapine, an atypical antipsychotic commonly used in trauma/critical care for delirium, protects the BBB and attenuates hyperpermeability in TBI. METHOD: The effect of quetiapine on hyperpermeability was examined through molecular modeling, cellular models in vitro and small animal models in vivo...
July 5, 2018: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/29982163/spectroscopic-and-molecular-modelling-studies-on-glycation-modified-bovine-serum-albumin-with-cyanidin-3-o-glucoside
#15
Govindarajan Prasanna, Pu Jing
In this study, we report the glycation mediated effect of bovine serum albumin (BSA) on the molecular interaction mechanism of cyanidin-3-O-glucoside (C3G) by molecular modelling, Uv-visible spectroscopy, transmission electron microscopy (TEM), fluorescence spectroscopy, and circular dichroism spectroscopy studies. The structures of advanced glycation end-products (AGEs) modified BSA were modelled, energy minimized and analyzed for binding affinity by molecular docking studies using Autodock Vina. Glycation experiments are carried out using glucose and methylglyoxal to validate the molecular modelling results on the interaction of modified BSA with C3G...
June 28, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29959004/purification-characterization-molecular-modeling-and-docking-study-of-fish-waste-protease
#16
Saranya R, Jayapriya J, Tamil Selvi A
In the present study, the alkaline protease has been extracted from the fish processing waste using ammonium sulphate fractionation followed by ion-exchange chromatography on sephadex G-25 and on DEAE column with a 4.0 fold increase in purification of yield 7.7%. The molecular weight of the purified protease was found to be 33 kDa as determined by SDS-PAGE. The optimum temperature was found to be 30 °C at pH 8. The activation energy (Ea ) for casein hydrolysis and temperature quotient (Q10 ) was found to be 38...
June 26, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29956231/quantifying-small-molecule-binding-interactions-with-dna-nanostructures
#17
Xuye Lang, Yingning Gao, Ian Wheeldon
DNA nanostructures and hybrid DNA-protein materials are attractive solutions to many applications in biotechnology and material science because of their controllable molecule-level features. Critical to a complete description and characterization of these technologies is the quantification of binding affinity between DNA nanostructures and small molecules relevant to the application at hand. This protocols chapter described a series of experimental and in silico analyses that can be used to described and quantify ligand binding interactions between DNA nanostructures (DNA DX tiles), short double stranded DNA fragments, and arbitrary small molecules...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29954088/-in-silico-screening-of-isocitrate-lyase-for-novel-anti-buruli-ulcer-natural-products-originating-from-africa
#18
Samuel K Kwofie, Bismark Dankwa, Emmanuel A Odame, Francis E Agamah, Lady P A Doe, Joshua Teye, Odame Agyapong, Whelton A Miller, Lydia Mosi, Michael D Wilson
Buruli ulcer (BU) is caused by Mycobacterium ulcerans and is predominant in both tropical and subtropical regions. The neglected debilitating disease is characterized by chronic necrotizing skin lesions attributed to a mycolactone, which is a macrolide toxin secreted by M. ulcerans . The preferred treatment is surgical excision of the lesions followed by a prolonged combination antibiotic therapy using existing drugs such as rifampicin and streptomycin or clarithromycin. These antibiotics appear not to be adequately potent and efficacious against persistent and late stage ulcers...
June 27, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29948580/synthesis-docking-and-anticancer-activity-of-azo-linked-hybrids-of-1-3-4-thia-oxadiazoles-with-cyclic-imides
#19
Priyanka Bhatt, Manoj Kumar, Anjali Jha
A series of novel analogues based on a diazole-imide pharmacophore were synthesized by diazotizing substituted 1,3,4-thia-/oxadiazol-2-amines and subsequently coupling the resulting diazonium salts with N-substituted cyclic imides. The resulting compounds C1 to C28 were characterized by various spectral methods, viz. IR, NMR and mass spectroscopy. All the synthesized compounds were tested against two human cancer cell lines: human breast adenocarcinoma cell line MCF-7 and colorectal adenocarcinoma cell line HT-29...
June 8, 2018: Molecular Diversity
https://www.readbyqxmd.com/read/29945503/proposing-drug-fragments-for-dengue-virus-ns5-protein
#20
Amr Alhossary, Yaw Awuni, Chee Keong Kwoh, Yuguang Mu
Dengue fever is a febrile illness caused by Dengue Virus, which belongs to the Flaviviridae family. Among its proteome, the nonstructural protein 5 (NS5) is the biggest and most conserved. It has a primer-independent RNA-dependent RNA polymerase (RdRp) domain at its C-Terminus. Zou et al. studied the biological relevance of the two conserved cavities (named A and B) within the NS5 proteins of dengue virus (DENV) and West Nile Virus (WNV) using mutagenesis and revertant analysis and found four mutations located at cavity B having effects on viral replication...
June 2018: Journal of Bioinformatics and Computational Biology
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