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https://www.readbyqxmd.com/read/29139502/development-of-the-first-model-of-a-phosphorylated-atp-mg-2-containing-b-raf-monomer-by-molecular-dynamics-simulations-a-tool-for-structure-based-design
#1
Viola Previtali, Cristina Trujillo, Jean-Charles Boisson, Hassan Khartabil, Eric Hénon, Isabel Rozas
A model of phosphorylated and ATP-containing B-Raf protein kinase is needed as a tool for the structure-based design of new allosteric inhibitors, since no crystal structure of such a system has been resolved. Here, we present the development of such a model as well as a thorough analysis of its structural features. This model was prepared using a systematic molecular dynamics approach considering the presence or absence of both the phosphate group at the Thr599 site and the ATP molecule. Then, different structural features (i...
November 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29138965/molecular-dynamics-and-integrated-pharmacophore-based-identification-of-dual-formula-see-text-inhibitors
#2
Maninder Kaur, Pankaj Kumar Singh, Manjinder Singh, Renu Bahadur, Om Silakari
Despite increase in the understanding of the pathogenesis of rheumatoid arthritis (RA), it remains a tough challenge. The advent of kinases involved in key intracellular pathways in pathogenesis of RA may provide a new phase of drug discovery for RA. The present study is aimed to identify dual JAK3/[Formula: see text] inhibitors by developing an optimum pharmacophore model integrating the information revealed by ligand-based pharmacophore models and structure-based pharmacophore models (SBPMs). For JAK3 inhibitors, the addition of an aromatic ring feature and for [Formula: see text] the addition of a hydrophobic feature proposed by SBPMs lead to five-point pharmacophore (i...
November 14, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/29138488/structural-basis-of-adaptor-mediated-protein-degradation-by-the-tail-specific-pdz-protease-prc
#3
Ming-Yuan Su, Nilanjan Som, Chia-Yun Wu, Shih-Chieh Su, Yi-Ting Kuo, Lu-Chu Ke, Meng-Ru Ho, Shiou-Ru Tzeng, Ching-Hao Teng, Dominique Mengin-Lecreulx, Manjula Reddy, Chung-I Chang
Peptidoglycan (PG) is a highly cross-linked, protective mesh-like sacculus that surrounds the bacterial cytoplasmic membrane. Expansion of PG is tightly coupled to growth of a bacterial cell and requires hydrolases to cleave the cross-links for insertion of nascent PG material. In Escherichia coli, a proteolytic system comprising the periplasmic PDZ-protease Prc and the lipoprotein adaptor NlpI contributes to PG enlargement by regulating cellular levels of MepS, a cross-link-specific hydrolase. Here, we demonstrate how NlpI binds Prc to facilitate the degradation of its substrate MepS by structural and mutational analyses...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29138424/structure-function-relationships-in-abcg2-insights-from-molecular-dynamics-simulations-and-molecular-docking-studies
#4
Ricardo J Ferreira, Cátia A Bonito, M Natália D S Cordeiro, Maria-José U Ferreira, Daniel J V A Dos Santos
Efflux pumps of the ATP-binding cassette transporters superfamily (ABC transporters) are frequently involved in the multidrug-resistance (MDR) phenomenon in cancer cells. Herein, we describe a new atomistic model for the MDR-related ABCG2 efflux pump, also named breast cancer resistance protein (BCRP), based on the recently published crystallographic structure of the ABCG5/G8 heterodimer sterol transporter, a member of the ABCG family involved in cholesterol homeostasis. By means of molecular dynamics simulations and molecular docking, a far-reaching characterization of the ABCG2 homodimer was obtained...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138086/eugenol-derivatives-prospectively-inhibit-l-asparaginase-a-heady-target-protein-of%C3%A2-salmonella-typhimurium
#5
Archana Vimal, Anubhuti Jha, Awanish Kumar
Salmonella typhimurium is the causative agent of severe human infections and mortality throughout the world. Pacing advent of new resistance mechanisms in this microorganism exists, rendering treatment of infectious disease difficult. Ciprofloxacin is no longer considered the first choice of antimicrobial agent due to the emergence of resistance. Therefore, the need for scenario is to find out novel drug target and its potential inhibitor to fight against this pathogen. The present study was undertaken to find out a novel drug target and its inhibitor for improving the current therapeutic methods for treating Salmonella infections...
November 11, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29137330/virtual-screening-approach-to-identifying-influenza-virus-neuraminidase-inhibitors-using-molecular-docking-combined-with-machine-learning-based-scoring-function
#6
Li Zhang, Hai-Xin Ai, Shi-Meng Li, Meng-Yuan Qi, Jian Zhao, Qi Zhao, Hong-Sheng Liu
In recent years, an epidemic of the highly pathogenic avian influenza H7N9 virus has persisted in China, with a high mortality rate. To develop novel anti-influenza therapies, we have constructed a machine-learning-based scoring function (RF-NA-Score) for the effective virtual screening of lead compounds targeting the viral neuraminidase (NA) protein. RF-NA-Score is more accurate than RF-Score, with a root-mean-square error of 1.46, Pearson's correlation coefficient of 0.707, and Spearman's rank correlation coefficient of 0...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136820/fluorescent-ligand-fishing-combination-with-in-situ-imaging-and-characterizing-to-screen-hsp-90-inhibitors-from-curcuma-longa-l-based-on-inp-zns-quantum-dots-embedded-mesoporous-nanoparticles
#7
Yue Hu, Anchen Fu, Zhaoyi Miao, Xiaojing Zhang, Tianlin Wang, An Kang, Jinjun Shan, Dong Zhu, Wei Li
Although ligand fishing has been shown to be an efficient technique for the identification of bioactive components from complex mixtures such as natural products, it cannot be applied to biomedical image processing. Herein, a specific fluorescent ligand fishing combined with in situ imaging approach is presented for the identification of heat shock protein 90 (Hsp 90) inhibitors from complex matrixes, Curcuma longa L., using N-terminus immobilized Hsp 90α functionalized InP/ZnS quantum dots embedded mesoporous nanoparticles (i...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136547/natural-products-used-as-a-chemical-library-for-protein-protein-interaction-targeted-drug-discovery
#8
Xuemei Jin, Kyungro Lee, Nam Hee Kim, Hyun Sil Kim, Jong In Yook, Jiwon Choi, Kyoung Tai No
Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery...
October 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29136249/natural-polyphenol-chlorogenic-acid-protects-against-acetaminophen-induced-hepatotoxicity-by-activating-erk-nrf2-antioxidative-pathway
#9
Mengjuan Wei, Zhiyong Zheng, Liang Shi, Yao Jin, Lili Ji
Hepatotoxicity due to acetaminophen (APAP) overdose is a leading cause of drug-induced acute liver failure in clinic. Chlorogenic acid (CGA), a dietary polyphenol, was reported to prevent APAP-induced liver injury in our previous studies. This study aims to investigate the protection provided by CGA against APAP-induced hepatotoxicity via focusing on nuclear factor erythroid 2-related factor 2 (Nrf2) and extracellular regulated protein kinases (ERK)1/2. CGA prevented APAP-induced oxidative liver injury and enhanced Nrf2 activation in mice and in hepatocytes in vitro...
November 10, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29135976/loss-of-peri-wolffian-duct-stromal-frs2%C3%AE-expression-in-mice-leads-to-abnormal-ureteric-bud-induction-and-vesicoureteral-reflux
#10
Deepti Narla, Stacey B Slagle, Caitlin M Schaefer, Daniel S Bushnell, Pawan Puri, Carlton M Bates
BackgroundFibroblast growth factor receptor 2 (Fgfr2) deletion from murine peri-Wolffian duct stroma (ST) results in aberrant ureteric bud induction, abnormal ureteral insertion into the bladder, and high rates of vesicoureteral reflux (VUR). It is unclear which receptor docking protein(s) is/are responsible for Fgfr2 actions in these tissues. We investigated whether the docking protein, fibroblast receptor substrate 2α (Frs2α), had a role in peri-Wolffian duct ST similar to Fgfr2.MethodsWe conditionally deleted Frs2α in peri-Wolffian duct ST with a Tbx18cre mouse line (Frs2α(ST-/-))...
December 2017: Pediatric Research
https://www.readbyqxmd.com/read/29135958/novel-%C3%AE-%C3%AE-unsaturated-sophoridinic-derivatives-design-synthesis-molecular-docking-and-anti-cancer-activities
#11
Yiming Xu, Lichuan Wu, Hang Dai, Mingyan Gao, Haroon Ur Rashid, Haodong Wang, Peng Xie, Xu Liu, Jun Jiang, Lisheng Wang
Using sophoridine 1 and chalcone 3 as the lead compounds, a series of novel α, β-unsaturated sophoridinic derivatives were designed, synthesized, and evaluated for their in vitro cytotoxicity. Structure-activity relationship (SAR) analysis indicated that introduction of α, β-unsaturated ketone moiety and heterocyclic group might significantly enhance anticancer activity. Among the compounds, 2f and 2m exhibited potential effects against HepG-2 and CNE-2 human cancer cell lines. Furthermore, molecular docking studies were performed to understand possible docking sites of the molecules on the target proteins and the mode of binding...
November 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29135287/molecular-modelling-studies-in-explaining-the-higher-gpvi-antagonistic-activity-of-the-racemic-2-4-methoxyphenylsulfonyl-2-3-4-9-tetrahydro-1h-pyrido-3-4-b-indole-3-carboxamide-than-its-enantiomers
#12
S S Bhunia, A K Saxena
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25...
November 14, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29134510/drug-design-for-alk-positive-nsclc-an-integrated-pharmacophore-based-3d-qsar-and-virtual-screening-strategy
#13
Nivya James, V Shanthi, K Ramanathan
The increasing death rates related to anaplastic lymphoma kinase (ALK)-positive lung cancer culminated in a significant interest in the discovery of novel inhibitors for ALK. In the present research work, pharmacophore-based 3D QSAR modeling and virtual screening strategy have been carried out to address these issues. Initially, a five-point pharmacophore model was developed using the biological data of 50 compounds which includes an FDA-approved ALK inhibitor, crizotinib. Using the generated pharmacophore, a 3D QSAR model was developed and used as a query to screen the DrugBank database...
November 13, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29134430/modern-drug-design-the-implication-of-using-artificial-neuronal-networks-and-multiple-molecular-dynamic-simulations
#14
Oleksandr Yakovenko, Steven J M Jones
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org/ ). The challenge was focused on the ligands of the farnesoid X receptor (FXR), a highly flexible nuclear receptor of the cholesterol derivative chenodeoxycholic acid. FXR is considered an important therapeutic target for metabolic, inflammatory, bowel and obesity related diseases (Expert Opin Drug Metab Toxicol 4:523-532, 2015), but in the context of this competition it is also interesting due to the significant ligand-induced conformational changes displayed by the protein...
November 13, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29133831/protein-ligand-blind-docking-using-quickvina-w-with-inter-process-spatio-temporal-integration
#15
Nafisa M Hassan, Amr A Alhossary, Yuguang Mu, Chee-Keong Kwoh
"Virtual Screening" is a common step of in silico drug design, where researchers screen a large library of small molecules (ligands) for interesting hits, in a process known as "Docking". However, docking is a computationally intensive and time-consuming process, usually restricted to small size binding sites (pockets) and small number of interacting residues. When the target site is not known (blind docking), researchers split the docking box into multiple boxes, or repeat the search several times using different seeds, and then merge the results manually...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133810/selectivity-and-ligand-based-molecular-modeling-of-an-odorant-binding-protein-from-the-leaf-beetle-ambrostoma-quadriimpressum-coleoptera-chrysomelidae-in-relation-to-habitat-related-volatiles
#16
Yinliang Wang, Yincan Jin, Qi Chen, Ming Wen, Hanbo Zhao, Hongxia Duan, Bingzhong Ren
In this study, the most abundant and antenna-specific odorant-binding protein (OBP) of the elm pest A. quadriimpressum, AquaOBP4, was expressed and purified. The selectivity of AquaOBP4 was investigated by screening against a panel of 40 habitat-relevant compounds. Based on the obtained results, a homologous model of AquaOBP4 was established. This model indicated that AquaOBP4 is highly homologous to DmelOBP LUSH and includes two main binding sites. A docking analysis showed that four of five active ligands bound at Site 1, whereas the other ligand was situated at Site 2...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133047/discovery-of-new-potent-molecular-entities-able-to-inhibit-mpges-1
#17
Simone Di Micco, Stefania Terracciano, Vincenza Cantone, Katrin Fischer, Andreas Koeberle, Antonio Foglia, Raffaele Riccio, Oliver Werz, Ines Bruno, Giuseppe Bifulco
mPGES-1, a glutathione-dependent membrane protein is involved in the last step of PGE2 production and has been well recognized as a strategic target for the development of anti-inflammatory and anti-cancer agents. It has been proven to selectively control the PGE2 levels induced by inflammatory stimuli, with neither affecting PGE2 constitutively produced, nor homeostatic prostanoids, so that its modulation can represent a better strategy to control PGE2 related disorders, compared to the use of the classical anti-inflammatory drugs, endowed with severe side effects...
October 23, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29132840/d-peptides-as-inhibitors-of-pr3-membrane-interactions
#18
Ksenia Maximova, Tom Venken, Nathalie Reuter, Joanna Trylska
Proteinase 3 (PR3) is a neutrophil serine protease present in cytoplasmic granules but also expressed at the neutrophil surface where it mediates proinflammatory effects. Studies of the underlying molecular mechanisms have been hampered by the lack of inhibitors of the PR3 membrane anchorage. Indeed while there exist inhibitors of the catalytic activity of PR3, its membrane interfacial binding site (IBS) is distinct from its catalytic site. The IBS has been characterized both by mutagenesis experiments and molecular modeling...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29132796/old-drug-new-indication-olsalazine-sodium-reduced-serum-uric-acid-levels-in-mice-via-inhibiting-xanthine-oxidoreductase-activity
#19
Yanfen Niu, Hongjian Li, Lihui Gao, Hua Lin, Hsiangfu Kung, Marie Chia-Mi Lin, Kwong-Sak Leung, Man-Hon Wong, Wenyong Xiong, Ling Li
Hyperuricemia, a long-term purine metabolic disorder, is a well-known risk factor for gout, hypertension and diabetes. In maintaining normal whole-body purine levels, xanthine oxidase (XOD) is a key enzyme in the purine metabolic pathway, as it catalyzes the oxidation of hypoxanthine to xanthine and finally to uric acid. Here we used the protein-ligand docking software idock to virtually screen potential XOD inhibitors from 3167 approved small compounds/drugs. The inhibitory activities of the ten compounds with the highest scores were tested on XOD in vitro...
October 31, 2017: Journal of Pharmacological Sciences
https://www.readbyqxmd.com/read/29132266/in-silico-molecular-docking-and-simulation-studies-on-novel-chalcone-and-flavone-hybrid-derivatives-with-1-2-3-triazole-linkage-as-vital-inhibitors-of-plasmodium-falciparum-dihydroorotate-dehydrogenase
#20
Mahalakshmi Thillainayagam, Kullappan Malathi, Sudha Ramaiah
The structural motifs of chalcones, flavones and triazoles with varied substitutions have been studied for the anti-malarial activity. In this study, 25 novel derivatives of chalcone and flavone hybrid derivatives with 1, 2, 3 - triazole linkage are docked with Plasmodium falciparum dihydroorotate dehydrogenase to establish their inhibitory activity against Plasmodium falciparum. The best binding conformation of the ligands at the catalytic site of dihydroorotate dehydrogenase are selected to characterize the best bound ligand using the best consensus score and the number of hydrogen bond interactions...
November 13, 2017: Journal of Biomolecular Structure & Dynamics
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