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https://www.readbyqxmd.com/read/29775968/in-silico-structure-prediction-and-inhibition-mechanism-studies-of-athda14-as-revealed-by-homology-modeling-docking-molecular-dynamics-simulation
#1
Ming-Lang Zhao, Wang Wang, Hu Nie, Sha-Sha Cao, Lin-Fang Du
Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots...
May 6, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29775303/simultaneous-targeting-of-rgd-integrins-and-dual-murine-double-minute-proteins-in-glioblastoma-multiforme
#2
Francesco Merlino, Simona Daniele, Valeria La Pietra, Salvatore Di Maro, Francesco Saverio Di Leva, Diego Brancaccio, Stefano Tomassi, Stefano Giuntini, Linda Cerofolini, Marco Fragai, Claudio Luchinat, Florian Reichart, Chiara Cavallini, Barbara Costa, Rebecca Piccarducci, Sabrina Taliani, Federico Da Settimo, Claudia Martini, Horst Kessler, Ettore Novellino, Luciana Marinelli
In the fight against Glioblastoma Multiforme, recent literature data have highlighted that integrin α5β1 and p53 are part of convergent pathways in the control of glioma apoptosis. This observation prompted us to seek a molecule able to simultaneously modulate both target families. Analyzing the results of a previous virtual screening against murine double minute 2 protein (MDM2), we envisaged that Arg-Gly-Asp (RGD)-mimetic molecules could be inhibitors of MDM2/4. Herein we present the discovery of compound 7, which inhibits both MDM2/4 and α5β1/αvβ3 integrins...
May 18, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29774657/cheminformatics-in-drug-discovery-an-industrial-perspective
#3
REVIEW
Hongming Chen, Thierry Kogej, Ola Engkvist
Cheminformatics has established itself as a core discipline within large scale drug discovery operations. It would be impossible to handle the amount of data generated today in a small molecule drug discovery project without persons skilled in cheminformatics. In addition, due to increased emphasis on "Big Data", machine learning and artificial intelligence, not only in the society in general, but also in drug discovery, it is expected that the cheminformatics field will be even more important in the future...
May 18, 2018: Molecular Informatics
https://www.readbyqxmd.com/read/29772045/ocular-tolerance-of-contemporary-electronic-display-devices
#4
Andrew J Clark, Paul Yang, Khizer R Khaderi, Andrew A Moshfeghi
Electronic displays have become an integral part of life in the developed world since the revolution of mobile computing a decade ago. With the release of multiple consumer-grade virtual reality (VR) and augmented reality (AR) products in the past 2 years utilizing head-mounted displays (HMDs), as well as the development of low-cost, smartphone-based HMDs, the ability to intimately interact with electronic screens is greater than ever. VR/AR HMDs also place the display at much closer ocular proximity than traditional electronic devices while also isolating the user from the ambient environment to create a "closed" system between the user's eyes and the display...
May 1, 2018: Ophthalmic Surgery, Lasers & Imaging Retina
https://www.readbyqxmd.com/read/29770817/the-dietary-compound-luteolin-inhibits-pancreatic-cancer-growth-by-targeting-bcl-2
#5
Zhimei Li, Yiyuan Zhang, Lixia Chen, Hua Li
Overexpression of the prosurvival protein BCL-2 contributes to malignant cell initiation, progression and resistance to treatment. Agents that function as its natural antagonists targeting BCL-2 must provide therapeutic benefit. In SW1990 pancreatic cancer cells, amplified BCL-2 was observed, which was believed to offer advantages for malignant cell survival and lead to poor patient outcome. Using structure-based virtual ligand screening, luteolin was found to be a natural small-molecule inhibitor of BCL-2, which exhibited dose-response proapoptosis activity in a BCL-2 dependent manner in vitro...
May 17, 2018: Food & Function
https://www.readbyqxmd.com/read/29767453/optimizing-antimicrobial-peptide-dendrimers-in-chemical-space
#6
Thissa Siriwardena, Alice Capecchi, Bee-Ha Gan, Xian Jin, Runze He, Dengwen Wei, Lan Ma, Thilo Köhler, Christian van Delden, Sacha Javor, Jean-Louis Reymond
Here we used nearest neighbor searches in chemical space to improve the activity of antimicrobial peptide dendrimer (AMPD) G3KL and identified dendrimer T7 with an expanded activity range against Gram-negative pathogenic bacteria including Klebsiellae pneumoniae, increased serum stability and promising activity in an in vivo infection model against a multidrug resistant strain of Acinetobacter baumannii. Imaging, spectroscopic studies and a structural model from molecular dynamics simulations suggest that T7 acts by membrane disruption...
May 16, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29766737/identification-of-small-molecule-egfr-allosteric-inhibitors-by-high-throughput-docking
#7
Fabiana Caporuscio, Annachiara Tinivella, Valentina Restelli, Marta S Semrau, Luca Pinzi, Paola Storici, Massimo Broggini, Giulio Rastelli
AIM: The EGFR inhibitors represent the first-line treatment of non-small-cell lung cancer. However, the emergence of resistance urgently requires the development of new inhibitors targeting drug-resistant mutants. METHODOLOGY: A recently released structure of an EGFR kinase domain in complex with an allosteric inhibitor and a mutant protein model derived from it were used to set up a low-cost high-throughput docking protocol for the fast identification of EGFR allosteric inhibitors...
May 16, 2018: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/29764677/a-novel-in-house-mixed-mode-solid-phase-extraction-of-urine-for-the-determination-of-16-basic-drugs-by-hplc-ion-trap-ms
#8
Giacomo Musile, Lucia Cenci, Elena Piletska, Rossella Gottardo, Alessandra M Bossi, Federica Bortolotti
The aim of the present work was to develop a novel in-house mixed-mode SPE sorbent to be used for the HPLC-Ion TrapMS determination of 16 basic drugs in urine. By using a computational modelling, a virtual monomer library was screened identifying three suitable functional monomers, methacrylic acid (MAA), itaconic acid (IA) and 2-acrylamide-2-methylpropane sulfonic acid (AMPSA), respectively. Three different sorbents were then synthetized based on these monomers, and using as cross-linker trimethylolpropane trimethacrylate (TMPTMA)...
May 9, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29763730/virtual-screening-of-plant-compounds-and-nonsteroidal-anti-inflammatory-drugs-for-inhibition-of-quorum-sensing-and-biofilm-formation-in-salmonella
#9
Felipe Alves de Almeida, Erika Lorena Giraldo Vargas, Deisy Guimarães Carneiro, Uelinton Manoel Pinto, Maria Cristina Dantas Vanetti
Salmonella belongs to the Enterobacteriaceae family which is widely distributed in the environment due to its adaptive capacity to stress conditions. In addition, Salmonella is able to perform a type of cell-to-cell communication called quorum sensing, which leads to differential gene expression. The quorum sensing system mediated by AI-1, acyl homoserine lactones (AHLs), is incomplete in Salmonella because the luxI homolog gene, which encodes for AI-1 synthase, is missing in the genome. However, a homologue of LuxR, known as SdiA, is present and allows the detection of signaling molecules produced by other species of bacteria, leading to regulation of gene expression, mainly related to virulence and biofilm formation...
May 12, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29763636/inhibition-of-cox-2-mpges-1-and-5-lox-in-macrophages-by-leonurine-ameliorates-monosodium-urate-crystal-induced-inflammation
#10
Yanzhuo Liu, Chenfan Duan, Honglei Chen, Chenlong Wang, Xiaoxiao Liu, Miao Qiu, Honglin Tang, Feng Zhang, Xiaoyang Zhou, Jing Yang
Cyclooxygenase-2 (COX-2), 5-lipoxygenase (5-LOX) and microsomal prostaglandin E synthase-1 (mPGES-1)-derived eicosanoids play an essential role in human inflammatory disorders. Here, we investigated whether inhibition of COX-2/mPGES-1 and 5-LOX in macrophages by leonurine ameliorates monosodium urate (MSU) crystal-induced inflammation. Virtual screening assay and in vitro enzyme inhibition assay showed that leonurine was a potential inhibitor of COX-2, mPGES-1 and 5-LOX. Compared with COX-2 inhibitor celecoxib, leonurine (30 mg/kg) significantly decreased ankle perimeter, gait score and neutrophil number in synovial fluid in MSU crystal-treated rats, accompanied with the decreased expression of COX-2, mPGES-1 and 5-LOX and production of prostaglandin E2 (PGE2 ) and leukotriene B4 (LTB4 ) in the synovial fluid macrophages...
May 15, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29761826/computational-discovery-of-potent-drugs-to-improve-the-treatment-of-pyrazinamide-resistant-mycobacterium-tuberculosis-mutants
#11
Manaswini Jagadeb, Surya N Rath, Avinash Sonawane
Emergence of multi-drug resistance tuberculosis has become a serious health problem globally. Accumulation of mutations in the drug target led to the development of multi-drug resistant mycobacterial strains that have made most of the conventional drugs ineffective. Hence, there is desperate need for the development of new therapeutic strategies. Here, we focused on the analysis of mutations in Mycobacterium tuberculosis (Mtb) PncA (pyrazinamidase) that is responsible for resistance against first-line anti-tuberculosis pyrazinamide (PZA) drug...
May 15, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29761098/discovery-of-natural-products-as-novel-and-potent-fxr-antagonists-by-virtual-screening
#12
Yanyan Diao, Jing Jiang, Shoude Zhang, Shiliang Li, Lei Shan, Jin Huang, Weidong Zhang, Honglin Li
Farnesoid X receptor (FXR) is a member of nuclear receptor family involved in multiple physiological processes through regulating specific target genes. The critical role of FXR as a transcriptional regulator makes it a promising target for diverse diseases, especially those related to metabolic disorders such as diabetes and cholestasis. However, the underlying activation mechanism of FXR is still a blur owing to the absence of proper FXR modulators. To identify potential FXR modulators, an in-house natural product database (NPD) containing over 4,000 compounds was screened by structure-based virtual screening strategy and subsequent hit-based similarity searching method...
2018: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29756561/advances-in-the-treatment-of-explicit-water-molecules-in-docking-and-binding-free-energy-calculations
#13
Xiao Hu, Irene Maffucci, Alessandro Contini
BACKGROUND: The inclusion of direct effects mediated by water during the ligand-receptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions...
May 13, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29756458/evaluation-of-the-effects-of-adding-vibrotactile-feedback-to-myoelectric-prosthesis-users-on-performance-and-visual-attention-in-a-dual-task-paradigm
#14
Eitan Raveh, Jason Friedman, Sigal Portnoy
OBJECTIVE: To evaluate the effects of adding vibrotactile feedback to myoelectric prosthesis users on the performance time and visual attention in a dual-task paradigm. DESIGN: A repeated-measures design with a counterbalanced order of two conditions. SETTING: Laboratory setting. SUBJECTS: Transradial amputees using a myoelectric prosthesis with normal or corrected eyesight ( N = 12, median age = 65 ± 13 years)...
May 1, 2018: Clinical Rehabilitation
https://www.readbyqxmd.com/read/29755970/how-to-achieve-better-results-using-pass-based-virtual-screening-case-study-for-kinase-inhibitors
#15
Pavel V Pogodin, Alexey A Lagunin, Anastasia V Rudik, Dmitry A Filimonov, Dmitry S Druzhilovskiy, Mark C Nicklaus, Vladimir V Poroikov
Discovery of new pharmaceutical substances is currently boosted by the possibility of utilization of the Synthetically Accessible Virtual Inventory (SAVI) library, which includes about 283 million molecules, each annotated with a proposed synthetic one-step route from commercially available starting materials. The SAVI database is well-suited for ligand-based methods of virtual screening to select molecules for experimental testing. In this study, we compare the performance of three approaches for the analysis of structure-activity relationships that differ in their criteria for selecting of "active" and "inactive" compounds included in the training sets...
2018: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29754957/pharmacological-inhibition-of-the-ubiquitin-ligase-rnf5-rescues-f508del-cftr-in-cystic-fibrosis-airway-epithelia
#16
Elvira Sondo, Federico Falchi, Emanuela Caci, Loretta Ferrera, Elisa Giacomini, Emanuela Pesce, Valeria Tomati, Sine Mandrup Bertozzi, Luca Goldoni, Andrea Armirotti, Roberto Ravazzolo, Andrea Cavalli, Nicoletta Pedemonte
In cystic fibrosis (CF), deletion of phenylalanine 508 (F508del) in the CFTR channel is associated with misfolding and premature degradation of the mutant protein. Among the known proteins associated with F508del-CFTR processing, the ubiquitin ligase RNF5/RMA1 is particularly interesting. We previously demonstrated that genetic suppression of RNF5 in vivo leads to an attenuation of intestinal pathological phenotypes in CF mice, validating the relevance of RNF5 as a drug target for CF. Here, we used a computational approach, based on ligand docking and virtual screening, to discover inh-02, a drug-like small molecule that inhibits RNF5...
April 26, 2018: Cell Chemical Biology
https://www.readbyqxmd.com/read/29752576/in-silico-docking-and-molecular-dynamics-simulation-of-3-dehydroquinate-synthase-dhqs-from-mycobacterium-tuberculosis
#17
Mustafa Alhaji Isa, Rita Singh Majumdhar, Shazia Haider
The shikimate pathway is as an attractive target because it is present in bacteria, algae, fungi, and plants but does not occur in mammals. In Mycobacterium tuberculosis (MTB), the shikimate pathway is integral to the biosynthesis of naphthoquinones, menaquinones, and mycobactin. In these study, novel inhibitors of 3-dehydroquinate synthase (DHQS), an enzyme that catalyzes the second step of the shikimate pathway in MTB, were determined. 12,165 compounds were selected from two public databases through virtual screening and molecular docking analysis using PyRx 8...
May 11, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29752249/virtual-antenatal-encounter-and-standardized-simulation-assessment-vanessa-pilot-study
#18
Patrick Motz, Megan Gray, Taylor Sawyer, Jennifer Kett, Douglas Danforth, Kellen Maicher, Rachel Umoren
BACKGROUND: Prenatal counseling at the limits of newborn viability involves sensitive interactions between neonatal providers and families. Empathetic discussions are currently learned through practice in times of high stress. Decision aids may help improve provider communication but have not been universally adopted. Virtual standardized patients are increasingly recognized as a modality for education, but prenatal counseling simulations have not been described. To be valuable as a tool, a virtual patient would need to accurately portray emotions and elicit a realistic response from the provider...
May 11, 2018: JMIR Serious Games
https://www.readbyqxmd.com/read/29751047/identification-of-novel-bioinspired-synthetic-mosquito-repellents-by-combined-ligand-based-screening-and-obp-structure-based-molecular-docking
#19
Trias Thireou, Georgia Kythreoti, Katerina E Tsitsanou, Konstantinos Koussis, Christina E Drakou, Julie Kinnersley, Thomas Kröber, Patrick M Guerin, Jing-Jiang Zhou, Kostas Iatrou, Elias Eliopoulos, Spyros E Zographos
In this work we report a fast and efficient virtual screening protocol for discovery of novel bioinspired synthetic mosquito repellents with lower volatility and, in all likelihood, increased protection time as compared with their plant-derived parental compounds. Our screening protocol comprises two filtering steps. The first filter is based on the shape and chemical similarity to known plant-derived repellents, whereas the second filter is based on the predicted similarity of the ligand's binding mode to the Anopheles gambiae odorant binding protein (AgamOBP1) relative to that of DEET and Icaridin to the same OBP...
May 8, 2018: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29750807/peer-review-of-health-research-funding-proposals-a-systematic-map-and-systematic-review-of-innovations-for-effectiveness-and-efficiency
#20
Jonathan Shepherd, Geoff K Frampton, Karen Pickett, Jeremy C Wyatt
OBJECTIVE: To investigate methods and processes for timely, efficient and good quality peer review of research funding proposals in health. METHODS: A two-stage evidence synthesis: (1) a systematic map to describe the key characteristics of the evidence base, followed by (2) a systematic review of the studies stakeholders prioritised as relevant from the map on the effectiveness and efficiency of peer review 'innovations'. Standard processes included literature searching, duplicate inclusion criteria screening, study keyword coding, data extraction, critical appraisal and study synthesis...
2018: PloS One
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