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Protein-protein docking

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https://www.readbyqxmd.com/read/29475181/impact-of-the-alkyl-chain-length-on-binding-of-imidazolium-based-ionic-liquids-to-bovine-serum-albumin
#1
Mengyue Zhang, Ying Wang, Hongmei Zhang, Jian Cao, Zhenghao Fei, Yanqing Wang
The effects of six imidazolium-based ionic liquids (ILs) with different alkyl chain length ([Cn Mim]Cl, n=2, 4, 6, 8, 10, 12) on the structure and functions of bovine serum albumin (BSA) were studied by multi-spectral methods and molecular docking. ILs with the longer alkyl chain length have the stronger binding interaction with BSA and the greater conformational damage to protein. The effects of ILs on the functional properties of BSA were further studied by the determination of non-enzyme esterase activity, β-fibrosis and other properties of BSA...
February 14, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29475176/rational-design-of-methicillin-resistance-staphylococcus-aureus-inhibitors-through-3d-qsar-molecular-docking-and-molecular-dynamics-simulations
#2
Srilata Ballu, Ramesh Itteboina, Sree Kanth Sivan, Vijjulatha Manga
Staphylococcus aureus is a gram positive bacterium. It is the leading cause of skin and respiratory infections, osteomyelitis, Ritter's disease, endocarditis, and bacteraemia in the developed world. We employed combined studies of 3D QSAR, molecular docking which are validated by molecular dynamics simulations and in silico ADME prediction have been performed on Isothiazoloquinolones inhibitors against methicillin resistance Staphylococcus aureus. Three-dimensional quantitative structure-activity relationship (3D-QSAR) study was applied using comparative molecular field analysis (CoMFA) with Q2 of 0...
December 20, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29475061/a-fungal-metabolite-zearalenone-as-a-cftr-inhibitor-and-potential-therapy-of-secretory-diarrheas
#3
Paradorn Muangnil, Saravut Satitsri, Kwanruthai Tadpetch, Patchreenart Saparpakorn, Varanuj Chatsudthipong, Supa Hannongbua, Vatcharin Rukachaisirikul, Chatchai Muanprasat
Overstimulation of CFTR-mediated Cl- secretion plays an important role in the pathogenesis of secretory diarrheas, which remain an important global health problem. This study aimed to identify inhibitors of CFTR-mediated Cl- secretion from a library of fungus-derived compounds and to evaluate their pharmacological properties and anti-diarrheal utility. We identified zearalenone, 7'-dehydrozearalenone and 8'-hydroxyzearalenone isolated from the seagrass-derived fungus Fusarium sp. PSU-ES123 as inhibitors of CFTR-mediated Cl- secretion in human intestinal epithelial (T84) cells...
February 20, 2018: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29475050/cyanidin-3-o-glucoside-functions-like-chemical-chaperone-and-attenuates-the-glycation-mediated-amyloid-formation-in-albumin
#4
Govindarajan Prasanna, Pu Jing
In this study, chemical chaperone like function of cyanidin-3-O-glucoside (C3G) was investigated through fluorescence spectroscopy, UV-visible spectroscopy, circular dichroism spectroscopy, confocal microscopy, scanning electron microscopy and molecular docking studies. Early and advanced glycation inhibitory effect was evaluated by fluorescence spectroscopy and agarose gel electrophoresis. Amyloids were investigated based on their propensity to bind Congo Red (CR) and Thioflavin T (ThT) by multiple microscopic approaches...
February 20, 2018: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29474831/comparative-genomic-analysis-of-rickettsia-rickettsii-for-the-identification-of-drug-and-vaccine-targets-tolc-as-a-proposed-candidate-for-case-study
#5
Pramod Kumar Maurya, Swati Singh, Ashutosh Mani
Antibiotic resistance is increasing rapidly in pathogenic organisms, creating more complications for treatment of diseases. Rocky Mountain spotted fever (RMSF) is a neglected tropical disease in humans caused by Rickettsia rickettsii for which no effective therapeutic is available. Subtractive genomics methods facilitate the characterization of non-homologous essential proteins that could be targeted for the discovery of potential therapeutic compounds against R. rickettsii to combat RMSF. Present study followed an in-silico based methodology, involving scanning and filtering the complete proteome of Rickettsia rickettsii by using several prioritization parameters in the search of potential candidates for drug development...
February 20, 2018: Acta Tropica
https://www.readbyqxmd.com/read/29474495/in-silico-and-in-vitro-studies-of-the-reduction-of-unsaturated-%C3%AE-%C3%AE-bonds-of-trans-2-hexenedioic-acid-and-6-amino-trans-2-hexenoic-acid-important-steps-towards-biobased-production-of-adipic-acid
#6
Emma Karlsson, Jae Ho Shin, Gunnar Westman, Leif A Eriksson, Lisbeth Olsson, Valeria Mapelli
The biobased production of adipic acid, a precursor in the production of nylon, is of great interest in order to replace the current petrochemical production route. Glucose-rich lignocellulosic raw materials have high potential to replace the petrochemical raw material. A number of metabolic pathways have been proposed for the microbial conversion of glucose to adipic acid, but achieved yields and titers remain to be improved before industrial applications are feasible. One proposed pathway starts with lysine, an essential metabolite industrially produced from glucose by microorganisms...
2018: PloS One
https://www.readbyqxmd.com/read/29473325/cheminformatics-analysis-of-dynamic-wnk-inhibitor-interactions
#7
Melaine A Kuenemann, Denis Fourches
The With-No-Lysine (WNK) serine/threonine kinase family constitutes a unique and distinctive branch of the kinome. The four proteins of this family (WNK1/2/3/4) are involved in blood pressure regulation, body fluid, and electrolyte homeostasis. Herein, we modeled and analyzed the binding modes of all publicly-available small orthosteric and allosteric binders (including WNK463 and WNK467) experimentally tested towards any of the WNK family member. To do so, we relied on state-of-the-art cheminformatics approaches including structure-based molecular docking and molecular dynamics simulations...
February 23, 2018: Molecular Informatics
https://www.readbyqxmd.com/read/29472595/a-motif-within-the-armadillo-repeat-of-parkinson-s-linked-lrrk2-interacts-with-fadd-to-hijack-the-extrinsic-death-pathway
#8
Nasia Antoniou, Dimitrios Vlachakis, Anna Memou, Emmanouela Leandrou, Polytimi-Eleni Valkimadi, Katerina Melachroinou, Diane B Re, Serge Przedborski, William T Dauer, Leonidas Stefanis, Hardy J Rideout
In experimental models, both in vivo and cellular, over-expression of Parkinson's linked mutant leucine-rich repeat kinase 2 (LRRK2) is sufficient to induce neuronal death. While several cell death associated proteins have been linked to LRRK2, either as protein interactors or as putative substrates, characterization of the neuronal death cascade remains elusive. In this study, we have mapped for the first time the domain within LRRK2 that mediates the interaction with FADD, thereby activating the molecular machinery of the extrinsic death pathway...
February 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29471050/the-protein-protein-interactions-between-amsacta-moorei-entomopoxvirus-amev-protein-kinases-pks-and-all-viral-proteins
#9
Mehtap Danismazoglu, Remziye Nalcacioglu, Hacer Muratoglu, Zihni Demirbag
Entomopoxviruses are an important group of viruses infecting only insects. They belong to Poxviridae which infect both invertebrates and vertebrates, including humans. Protein kinases are known to have roles at virus morphogenesis, host selectivity, the regulation of cell division and apoptosis in some vertebrate poxviruses. In this study, 2 protein kinases (PKs) (AMV153 and AMV197) of Amsacta moorei entomopoxvirus (AMEV) were investigated for the interactions among 230 viral proteins using yeast two-hybrid system (Y2H)...
February 19, 2018: Virus Research
https://www.readbyqxmd.com/read/29468973/molecular-docking-in-formulation-and-development
#10
Tejinder Kaur Marwaha, Ashwini Madgulkar, Mangesh Bhalekar, Kalyani Asgaonkar
In pharmaceutical research drug discovery and development process is time-consuming and expensive. In many cases, it produces incompetent results due to the failure of in vitro and in vivo conventional approaches. Before any new drug is placed in the market it must undergo rigorous testing to get FDA approval. Due to the several limitations imposed by the drug discovery process, in recent times in silico approaches are widely applied in this field. In this review we have compiled docking studies which has found it's applications to predict drug excipient interactions which in turn assist to increase protein stability; to determine enzyme peptide interactions which maybe further used in drug development studies; to determine the most stable drug inclusion complex; to analyze structure at molecular level that ascertain an increase in solubility, dissolution and in turn the bioavailability of the drug; to design a dosage form that amplify the drug discovery and development process...
February 18, 2018: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/29468962/plant-derived-polyphenols-in-human-health-biological-activity-metabolites-and-putative-molecular-targets
#11
Marilo Olivares-Vicente, Enrique Barrajon-Catalan, Maria Herranz-Lopez, Antonio Segura-Carretero, Jorge Joven, Jose Antonio Encinar, Vicente Micol
Edible plants such as Hibiscus sabdariffa, Lippia citriodora, Rosmarinus officinalis and Olea europaea, are rich in bioactive compounds that represent most of the phenolic compounds families and have exhibited potential benefits in human health. These plants have been commonly used in folk medicine for their potential therapeutic properties in human chronic diseases. Recent evidence on these plants leads to postulate that polyphenols may account for such effects. Nevertheless, the compounds or metabolites that are responsible for reaching the molecular targets are still unknown...
February 19, 2018: Current Drug Metabolism
https://www.readbyqxmd.com/read/29468960/the-discovery-of-antibacterial-natural-compound-based-on-peptide-deformylase
#12
Li Liang, Qianqian Zhou, Zhixiang Hao, Fanfan Wang, Yasheng Zhu, Qisi Lin, Jian Gao
BACKGROUND: In recent years, Staphylococcus aureus have developed resistance to medicines used for the treatment of human infections. Therefore, the search for antibacterial agents of high potency against Staphylococcus aureus is of great concern. Peptide deformylase (PDF), a metalloprotease catalyzing the removal of a formyl group from newly synthesized proteins, has been considered to be an important antibacterial drug target. OBJECTIVE: To discover novel antibacterial drugs based on Staphylococcus aureus peptide deformylase...
February 20, 2018: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/29468851/isolates-from-alpinia-officinarum-hance-attenuate-lps-induced-inflammation-in-hepg2-evidence-from-in-silico-and-in-vitro-studies
#13
Abdullah A Elgazar, Nabil M Selim, Nabil M Abdel-Hamid, Mohammed A El-Magd, Hala M El Hefnawy
In an attempt to connect the legacy of centuries of invaluable knowledge from traditional medicine and the current understanding to the molecular mechanism of diseases, we took the advantage of the emergence of in silico screening as a promising tool for identification of potential leads from libraries of natural products. Traditional Chinese Medicine database was subjected to structure based virtual screening for identification of anti-inflammatory compounds using the 3D crystal structure of p38 alpha mitogen activated protein kinase...
February 22, 2018: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/29464047/a-dock-derived-compound-against-laminin-receptor-37-lr-exhibits-anti-cancer-properties-in-a-prostate-cancer-cell-line-model
#14
Charles Samuel Umbaugh, Adriana Diaz-Quiñones, Manoel Figueiredo Neto, Joseph J Shearer, Marxa L Figueiredo
Laminin receptor (67 LR) is a 67 kDa protein derived from a 37 kDa precursor (37 LR). 37/67 LR is a strong clinical correlate for progression, aggression, and chemotherapeutic relapse of several cancers including breast, prostate, and colon. The ability of 37/67 LR to promote cancer cell aggressiveness is further increased by its ability to transduce physiochemical and mechanosensing signals in endothelial cells and modulate angiogenesis. Recently, it was demonstrated that 37/67 LR modulates the anti-angiogenic potential of the secreted glycoprotein pigment epithelium-derived factor (PEDF)...
January 19, 2018: Oncotarget
https://www.readbyqxmd.com/read/29463901/poly-adp-ribose-mediates-asymmetric-division-of-mouse-oocyte
#15
Bingteng Xie, Lu Zhang, Huiling Zhao, Qingyun Bai, Yong Fan, Xiaohui Zhu, Yang Yu, Rong Li, Xin Liang, Qing-Yuan Sun, Mo Li, Jie Qiao
Before fertilization, mammalian oocyte undergoes an asymmetric division which depends on eccentric positioning of the spindle at the oocyte cortex to form a polar body and an egg. Since the centriole is absent and, as a result, the polar array microtubules are not fully developed in oocytes, microtubules have seldom been considered as required for eccentric positioning of the spindle, while actin-related forces have instead been proposed to be primarily responsible for this process. However, the existing models are largely conflicting and the underlying mechanism of asymmetric division is still elusive...
February 20, 2018: Cell Research
https://www.readbyqxmd.com/read/29463017/identification-of-novel-protein-kinase-receptor-type-2-inhibitors-using-pharmacophore-and-structure-based-virtual-screening
#16
Josiane V Cruz, Moysés F A Neto, Luciane B Silva, Ryan da S Ramos, Josivan da S Costa, Davi S B Brasil, Cleison C Lobato, Glauber V da Costa, José Adolfo H M Bittencourt, Carlos H T P da Silva, Franco H A Leite, Cleydson B R Santos
The Protein Kinase Receptor type 2 (RIPK2) plays an important role in the pathogenesis of inflammatory diseases; it signals downstream of the NOD1 and NOD2 intracellular sensors and promotes a productive inflammatory response. However, excessive NOD2 signaling has been associated with various diseases, including sarcoidosis and inflammatory arthritis; the pharmacological inhibition of RIPK2 is an affinity strategy that demonstrates an increased expression of pro-inflammatory secretion activity. In this study, a pharmacophoric model based on the crystallographic pose of ponatinib, a potent RIPK2 inhibitor, and 30 other ones selected from the BindingDB repository database, was built...
February 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29462787/mechanistic-insights-into-transferable-polymyxin-resistance-among-gut-bacteria
#17
Yongchang Xu, Jingxia Lin, Tao Cui, Swaminath Srinivas, Youjun Feng
Polymyxins such as colistin are antibiotics used as a final line of defense in the management of infections with multidrug-resistant Gram-negative bacteria. Although natural resistance to polymyxins is rare, the discovery of a mobilized colistin resistance gene ( mcr-1 ) in gut bacteria has raised significant concern. As an intramembrane enzyme, MCR-1 catalyzes the transfer of phosphoethanolamine (PEA) to the 1 (or 4')-phosphate group of the lipid A moiety of lipopolysaccharide (LPS), thereby conferring colistin resistance...
February 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29462686/plga-nanoformulation-of-sparfloxacin-enhanced-antibacterial-activity-with-photoprotective-potential-under-ambient-uv-r-exposure
#18
Jyoti Singh, Ashish Dwivedi, Lipika Ray, Deepti Chopra, Divya Dubey, Ajeet K Srivastva, Smita Kumari, Randheer Kumar, Saroj Kumar Amar, Chandana Haldar, Ratan Singh Ray
Sparfloxacin (SPFX) is a broad spectrum antibiotic which inhibits bacterial DNA gyrase enzyme activity. However, photodegradation in the presence of UVA limits its antibacterial activity and induces phototoxicity. Thus, to encounter this problem, we have developed poly d,l-lactic-co- glycolic acid (PLGA) loaded SPFX nanoparticles. Here, we have performed a comparative antibacterial activity of SPFX and its nanoparticles (NPs) through molecular docking and plate sensitivity assay. Under environmental UVA exposure, photoexcited SPFX significantly generates ROS, DNA damage and mitochondrial mediated cell death in comparison to PLGA-SPFX-NPs (nano SPFX) in human skin cell line (HaCaT)...
February 17, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29462602/6-shogaol-induces-caspase-independent-paraptosis-in-cancer-cells-via-proteasomal-inhibition
#19
Divya Nedungadi, Anupama Binoy, Nanjan Pandurangan, Sanjay Pal, Bipin G Nair, Nandita Mishra
An α, β-unsaturated carbonyl compound of ginger, 6-Shogaol (6S), induced extensive cytoplasmic vacuolation and cell death in breast cancer cell (MDA-MB-231) and non-small lung cancer (A549) cells. In the presence of autophagic inhibitors the cells continued to exhibit cytoplasmic vacuolation and cell death clearly distinguishing it from the classic autophagic process. 6S induced death did not exhibit the characteristic apoptotic features like caspase cleavage, phosphatidyl serine exposure and DNA fragmentation...
February 17, 2018: Experimental Cell Research
https://www.readbyqxmd.com/read/29459424/the-role-of-adherens-junction-proteins-in-the-regulation-of-insulin-secretion
#20
Waruni C Dissanayake, Brie Sorrenson, Peter R Shepherd
In healthy individuals any rise in blood glucose levels is rapidly countered by the release of insulin from the β-cells of the pancreas which in turn promotes the uptake and storage of the glucose in peripheral tissues. The β-cells possess exquisite mechansims regulating the secretion of insulin to ensure that the correct amount of insulin is released. These mechanisms involve tight control of the movement of insulin containing secretory vesicles within the β-cells, initially preventing most vesicles being able to move to the plasma membrane...
February 19, 2018: Bioscience Reports
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