keyword
MENU ▼
Read by QxMD icon Read
search

Computational drug design

keyword
https://www.readbyqxmd.com/read/28645065/cross-validation-of-short-forms-of-the-screener-and-opioid-assessment-for-patients-with-pain-revised-soapp-r
#1
Matthew D Finkelman, Robert N Jamison, Ronald J Kulich, Stephen F Butler, William C Jackson, Niels Smits, Scott G Weiner
BACKGROUND: The Screener and Opioid Assessment for Patients with Pain-Revised (SOAPP-R) is a 24-item assessment designed to assist in the prediction of aberrant drug-related behavior (ADB) among patients with chronic pain. Recent work has created shorter versions of the SOAPP-R, including a static 12-item short form and two computer-based methods (curtailment and stochastic curtailment) that monitor assessments in progress. The purpose of this study was to cross-validate these shorter versions in two new populations...
June 13, 2017: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/28643003/recent-developments-in-solution-nuclear-magnetic-resonance-nmr-based-molecular-biology
#2
REVIEW
Joshua J Ziarek, Diego Baptista, Gerhard Wagner
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors...
June 23, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28641529/irna-2methyl-identify-rna-2-o-methylation-sites-by-incorporating-sequence-coupled-effects-into-general-pseknc-and-ensemble-classifier
#3
Wang-Ren Qiu, Shi-Yu Jiang, Bi-Qian Sun, Xuan Xiao, Xiang Cheng, Kuo-Chen Chou
OBJECTIVE: Being a kind of post-transcriptional modification (PTCM) in RNA, the 2'-O-methylation modification occurs in the processes of life development and disease formation as well. Accordingly, from the angles of both basic research and drug development, we are facing a challenging problem: given an uncharacterized RNA sequence formed by many nucleotides of A (adenine), C (cytosine), G (guanine), and U (uracil), which one can be of 2-O-methylation modification, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such a problem...
June 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28641198/combined-computational-experimental-approach-to-predict-blood-brain-barrier-bbb-permeation-based-on-green-salting-out-thin-layer-chromatography-supported-by-simple-molecular-descriptors
#4
Krzesimir Ciura, Mariusz Belka, Piotr Kawczak, Tomasz Bączek, Michał J Markuszewski, Joanna Nowakowska
The objective of this paper is to build QSRR/QSAR model for predicting the blood-brain barrier (BBB) permeability. The obtained models are based on salting-out thin layer chromatography (SOTLC) constants and calculated molecular descriptors. Among chromatographic methods SOTLC was chosen, since the mobile phases are free of organic solvent. As consequences, there are less toxic, and have lower environmental impact compared to classical reserved phases liquid chromatography (RPLC). During the study three stationary phase silica gel, cellulose plates and neutral aluminum oxide were examined...
June 3, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28638421/item-selection-and-content-validity-of-the-risk-factors-of-post-intubation-tracheal-stenosis-observation-questionnaire-for-icu-admitted-patients
#5
Roya Farzanegan, Behrooz Farzanegan, Maryam Alehashem, Mahdi Zangi, Sharareh R Niakan Kalhori, Kambiz Sheikhy, Habib Emami, Mohammad Behgam Shadmehr
BACKGROUND: Laryngotracheal stenosis as a late complication of prolonged endotracheal intubation is a life-threatening event. In order to determine the related risk factors for this complication, which may vary among different countries, designing a valid questionnaire is necessary. The aim of this study was to select the items and evaluate the face and content validities of a questionnaire developed for assessment of risk factors of post-intubation tracheal stenosis (PITS) in patients admitted in the intensive care unit...
2017: Tanaffos
https://www.readbyqxmd.com/read/28633119/polymer-grafted-magnetic-halloysite-nanotube-for-controlled-and-sustained-release-of-cationic-drug
#6
Meriem Fizir, Pierre Dramou, Kai Zhang, Cheng Sun, Chuong Pham-Huy, Hua He
In this research, novel polymer grafted-magnetic halloysite nanotubes with norfloxacin loaded (NOR-MHNTs) and controlled-release, was achieved by surface-initiated precipitation polymerization. The magnetic halloysite nanotubes exhibited better adsorption of NOR (72.10mgg(-1)) compared with the pristine HNTs (30.80mgg(-1)). Various parameters influencing the drug adsorption of the MHNTs for NOR were studied. Polymer grafted NOR-MHNTs has been designed using flexible docking in computer simulation to choose optimal monomers...
April 6, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28632395/design-synthesis-and-multitarget-biological-profiling-of-second-generation-anti-alzheimer-rhein-huprine-hybrids
#7
Francisco Javier Pérez-Areales, Nibal Betari, Antonio Viayna, Caterina Pont, Alba Espargaró, Manuela Bartolini, Angela De Simone, José Fernando Rinaldi Alvarenga, Belén Pérez, Raimon Sabate, Rosa Maria Lamuela-Raventós, Vincenza Andrisano, Francisco Javier Luque, Diego Muñoz-Torrero
AIM: Simultaneous modulation of several key targets of the pathological network of Alzheimer's disease (AD) is being increasingly pursued as a promising option to fill the critical gap of efficacious drugs against this condition. MATERIALS & METHODS: A short series of compounds purported to hit multiple targets of relevance in AD has been designed, on the basis of their distinct basicities estimated from high-level quantum mechanical computations, synthesized, and subjected to assays of inhibition of cholinesterases, BACE-1, and Aβ42 and tau aggregation, of antioxidant activity, and of brain permeation...
June 20, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28629518/analysis-of-the-asymmetry-of-activated-epo-receptor-enables-designing-small-molecule-agonists
#8
Frank Guarnieri
Amgen solved the high-resolution cocrystal structure of erythropoietin (EPO) bound to the extracellular part of the receptor (EPOR) in 1998, which reveals that the EPO-EPOR interaction surface is formed by 11 salt bridges, 17 H-bonds, and 2 hydrophobic clusters centered at a pair of crucial phenylalanines (F93). The EPOR has two domains, one that penetrates the membrane and a second extracellular domain that forms one arm of the binding site for the EPO ligand. The complete competent receptor-binding site is a homodimer of EPOR with the two arms forming a funnel-shaped cup where EPO binds...
2017: Vitamins and Hormones
https://www.readbyqxmd.com/read/28629155/repositioning-fda-drugs-as-potential-cruzain-inhibitors-from-trypanosoma-cruzi-virtual-screening-in-vitro-and-in-vivo-studies
#9
Isidro Palos, Edgar E Lara-Ramirez, Julio Cesar Lopez-Cedillo, Carlos Garcia-Perez, Muhammad Kashif, Virgilio Bocanegra-Garcia, Benjamin Nogueda-Torres, Gildardo Rivera
Chagas disease (CD) is a neglected disease caused by the parasite Trypanosoma cruzi, which affects underdeveloped countries. The current drugs of choice are nifurtimox and benznidazole, but both have severe adverse effects and less effectivity in chronic infections; therefore, the need to discover new drugs is essential. A computer-guided drug repositioning method was applied to identify potential FDA drugs (approved and withdrawn) as cruzain (Cz) inhibitors and trypanocidal effects were confirmed by in vitro and in vivo studies...
June 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28627775/ensemble-architecture-for-prediction-of-enzyme-ligand-binding-residues-using-evolutionary-information
#10
Priyadarshini P Pai, Rohit Kadam Dattatreya, Sukanta Mondal
Enzyme interactions with ligands are crucial for various biochemical reactions governing life. Over many years attempts to identify these residues for biotechnological manipulations have been made using experimental and computational techniques. The computational approaches have gathered impetus with the accruing availability of sequence and structure information, broadly classified into template-based and de novo methods. One of the predominant de novo methods using sequence information involves application of biological properties for supervised machine learning...
June 19, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28625755/multilevel-engineering-of-the-upstream-module-of-aromatic-amino-acid-biosynthesis-in-saccharomyces-cerevisiae-for-high-production-of-polymer-and-drug-precursors
#11
Miguel Suástegui, Chiam Yu Ng, Anupam Chowdhury, Wan Sun, Mingfeng Cao, Emma House, Costas D Maranas, Zengyi Shao
A multilevel approach was implemented in Saccharomyces cerevisiae to optimize the precursor module of the aromatic amino acid biosynthesis pathway, which is a rich resource for synthesizing a great variety of chemicals ranging from polymer precursor, to nutraceuticals and pain-relief drugs. To facilitate the discovery of novel targets to enhance the pathway flux, we incorporated the computational tool YEASTRACT for predicting novel transcriptional repressors and OptForce strain-design for identifying non-intuitive pathway interventions...
June 15, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28625366/feasibility-of-transcatheter-aortic-valve-replacement-in-low-risk-patients-with-symptomatic-severe-aortic-stenosis-rationale-and-design-of-the-low-risk-tavr-lrt-study
#12
Toby Rogers, Rebecca Torguson, Roshni Bastian, Paul Corso, Ron Waksman
BACKGROUND: Safety and effectiveness of transcatheter aortic valve replacement (TAVR) in low-risk patients with symptomatic severe aortic stenosis have not yet been established. HYPOTHESIS: Transcatheter aortic valve replacement is feasible in patients with symptomatic severe aortic stenosis and low risk for surgical aortic valve replacement. DESIGN: The LRT study is the first US Food and Drug Administration-approved Investigational Device Exemption prospective multicenter feasibility trial of TAVR in low-risk patients...
July 2017: American Heart Journal
https://www.readbyqxmd.com/read/28624475/oxidoreductases-on-their-way-to-industrial-biotransformations
#13
REVIEW
Angel T Martínez, Francisco J Ruiz-Dueñas, Susana Camarero, Ana Serrano, Dolores Linde, Henrik Lund, Jesper Vind, Morten Tovborg, Owik M Herold-Majumdar, Martin Hofrichter, Christiane Liers, René Ullrich, Katrin Scheibner, Giovanni Sannia, Alessandra Piscitelli, Cinzia Pezzella, Mehmet E Sener, Sibel Kılıç, Willem J H van Berkel, Victor Guallar, Maria Fátima Lucas, Ralf Zuhse, Roland Ludwig, Frank Hollmann, Elena Fernández-Fueyo, Eric Record, Craig B Faulds, Marta Tortajada, Ib Winckelmann, Jo-Anne Rasmussen, Mirjana Gelo-Pujic, Ana Gutiérrez, José C Del Río, Jorge Rencoret, Miguel Alcalde
Fungi produce heme-containing peroxidases and peroxygenases, flavin-containing oxidases and dehydrogenases, and different copper-containing oxidoreductases involved in the biodegradation of lignin and other recalcitrant compounds. Heme peroxidases comprise the classical ligninolytic peroxidases and the new dye-decolorizing peroxidases, while heme peroxygenases belong to a still largely unexplored superfamily of heme-thiolate proteins. Nevertheless, basidiomycete unspecific peroxygenases have the highest biotechnological interest due to their ability to catalyze a variety of regio- and stereo-selective monooxygenation reactions with H2O2 as the source of oxygen and final electron acceptor...
June 14, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28623462/in-silico-investigations-of-chemical-constituents-of-clerodendrum-colebrookianum-in-the-anti-hypertensive-drug-targets-rock-ace-and-pde5
#14
Hemant Arya, Safiulla Basha Syed, Sorokhaibam Sureshkumar Singh, Dinakar R Ampasala, Mohane Selvaraj Coumar
Understanding the molecular mode of action of natural product is a key step for developing drugs from them. In this regard, this study is aimed to understand the molecular-level interactions of chemical constituents of Clerodendrum colebrookianum Walp., with anti-hypertensive drug targets using computational approaches. The plant has ethno-medicinal importance for the treatment of hypertension and reported to show activity against anti-hypertensive drug targets-Rho-associated coiled-coil protein kinase (ROCK), angiotensin-converting enzyme, and phosphodiesterase 5 (PDE5)...
June 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28620979/an-application-of-cifap-for-predicting-the-binding-affinity-of-chk1-inhibitors-derived-from-2-aminothiazole-4-carboxamide
#15
Dilan Konyar, Ozlem Erdas, Ferda Nur Alpaslan, Erdem Buyukbingol
Investigation of protein-ligand interactions obtained from experiments has a crucial part in the design of newly discovered and effective drugs. Analyzing the data extracted from known interactions could help scientists to predict the binding affinities of promising ligands before conducting experiments. The objective of this study is to advance the CIFAP (compressed images for affinity prediction) method, which is relevant to a protein-ligand model, identifying 2D electrostatic potential images by separating the binding site of protein-ligand complexes and using the images for predicting the computational affinity information represented by pIC50 values...
June 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28615159/mobile-health-in-oncology-a-patient-survey-about-app-assisted-cancer-care
#16
Kerstin Anne Kessel, Marco Me Vogel, Carmen Kessel, Henning Bier, Tilo Biedermann, Helmut Friess, Peter Herschbach, Rüdiger von Eisenhart-Rothe, Bernhard Meyer, Marion Kiechle, Ulrich Keller, Christian Peschel, Roland M Schmid, Stephanie E Combs
BACKGROUND: In the last decade, the health care sector has been enriched by numerous innovations such as apps and connected devices that assist users in weight reduction and diabetes management. However, only a few native apps in the oncological context exist, which support patients during treatment and aftercare. OBJECTIVE: The objective of this study was to analyze patients' acceptance regarding app use and to investigate the functions of an oncological app that are most required, and the primary reasons for patients to refuse app-assisted cancer care...
June 14, 2017: JMIR MHealth and UHealth
https://www.readbyqxmd.com/read/28609624/in-silico-absorption-distribution-metabolism-excretion-and-pharmacokinetics-adme-pk-utility-and-best-practices-an-industry-perspective-from-the-international-consortium-for-innovation-through-quality-in-pharmaceutical-development
#17
Franco Lombardo, Prashant V Desai, Rieko Arimoto, Kelly E Desino, Holger Fischer, Christopher E Keefer, Carl Petersson, Susanne Winiwarter, Fabio Broccatelli
In silico tools to investigate absorption, distribution, metabolism, excretion and pharmacokinetics (ADME-PK) properties of new chemical entities are an integral part of the current industrial drug discovery paradigm. While many companies are active in the field, scientists engaged in this area don't necessarily share the same background and have limited resources when seeking guidance on how to initiate and maintain an in silico ADME-PK infrastructure in an industrial setting. This work summarizes the views of a group of industrial in silico and experimental ADME scientists, participating in the In Silico ADME Working Group, a subgroup of the International Consortium for Innovation through Quality in Pharmaceutical Development (IQ) Drug Metabolism Leadership Group...
June 13, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28608934/an-integrated-computational-framework-to-assess-the-mutational-landscape-of-%C3%AE-l-iduronidase-idua-gene
#18
Himani Tanwar, George Priya Doss C
Mucopolysaccharidosis type I is a lysosomal genetic disorder caused due to the deficiency of the α-L-iduronidase enzyme (IDUA). Mutations associated with IDUA lead to mild to severe forms of diseases characterized by different clinical features. In the present study, we first performed a comprehensive analysis using various in silico prediction tools to screen and prioritize the missense mutations or nonsynonymous SNPs (nsSNPs) associated with IDUA. Subsequently, statistical analysis was empowered to examine the predictive ability and accuracy of the in silico prediction tool results supporting the disease phenotype ranging from mild to severe...
June 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28605584/statistical-analysis-investigation-and-prediction-of-the-water-positions-in-the-binding-sites-of-proteins
#19
Wei Xiao, Zenghui He, Meijian Sun, Shiliang Li, Honglin Li
Water molecules play a crucial role in biomolecular associations by mediating a hydrogen bond network or filling spaces with van der Waals interactions. Although current drug design technologies have taken water molecule interactions into account, their applications are still limited to their reliance on either excessive computer resources or a particular potential energy model. Here, we introduce a statistical method that is based on experimentally-determined water molecules in the binding sites of high-resolution X-ray crystal structures to predict the potential hydration sites in the binding sites of a crystal structures of interest...
June 12, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28604250/synthesis-characterization-in-silico-admet-prediction-and-protein-binding-analysis-of-a-novel-zinc-ii-schiff-base-complex-application-of-multi-spectroscopic-and-computational-techniques
#20
Somaye Shahraki, Fereshteh Shiri, Maryam Saeidifar
By reaction of 1,2-diaminocyclohexane with the 2,3-butanedione monoxime in the presence of ZnCl2, a new Schiff base complex was obtained. This complex was characterized by elemental analyses, FT-IR, (1)H NMR, UV-Vis and conductivity measurements. The reactivity of this complex to human serum albumin (HSA) under simulative physiological conditions was studied by spectroscopic and molecular docking analysis. Experimental results at various temperatures indicated that the intrinsic fluorescence of protein was quenched through a static quenching mechanism...
June 12, 2017: Journal of Biomolecular Structure & Dynamics
keyword
keyword
84853
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"