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Protein-protein docking

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https://www.readbyqxmd.com/read/28735432/eucalyptol-sabinene-and-cinnamaldehyde-potent-inhibitors-of-salmonella-target-protein-l-asparaginase
#1
Archana Vimal, Dharm Pal, Timir Tripathi, Awanish Kumar
Salmonella typhimurium is a severe threat to human life. The treatment became more difficult with the emergence of multidrug resistance. In the present in silico study, a novel drug target L-asparaginase was tested against three ligands eucalyptol, sabinene, and cinnamaldehyde, major components of cardamom, nutmeg, and cinnamon, respectively. The lowest docking score was obtained for sabinene followed by eucalyptol and cinnamaldehyde i.e. -5.648, -3.939 and -3.469. The docking score of sabinene is also better than the standard drug, Ciprofloxacin (-4...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28734977/modulation-of-the-interaction-between-human-p450-3a4-and-b-megaterium-reductase-via-engineered-loops
#2
Silvia Castrignanò, Serena D'Avino, Giovanna Di Nardo, Gianluca Catucci, Sheila J Sadeghi, Gianfranco Gilardi
Chimerogenesis involving cytochromes P450 is a successful approach to generate catalytically self-sufficient enzymes. However, the connection between the different functional modules should allow a certain degree of flexibility in order to obtain functional and catalytically efficient proteins. We previously applied the molecular Lego approach to develop a chimeric P450 3A4 enzyme linked to the reductase domain of P450 BM3 (BMR). Three constructs were designed with the connecting loop containing no glycine, 3 glycine or 5 glycine residues and showed a different catalytic activity and coupling efficiency...
July 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28734205/identification-of-mycobacterium-tuberculosis-enoyl-acyl-carrier-protein-reductase-inhibitors-a-combined-in-silico-and-in-vitro-analysis
#3
Mohsin Y Lone, Mohd Athar, Vivek K Gupta, Prakash C Jha
Mycobacterium tuberculosis (Mtb), had developed evolutionary changes in its genome to adapt for survival and thereby generated multi-drug resistant strains. However, novel drug targets that remained unchanged for their biochemical role has impressed the research community to target such proteins. The comprehensive analysis of multiple protein targets has influenced us to make a consensus structural rule exploited by pharmacophore and other allied techniques from a large repository of protein structures. In this pursuit, we made a retrospective analysis of pharmacophores mapped from the tuberculosis structural proteome and identified unique patterns that can be employed for the novel molecules design...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28733815/structure-of-isolated-z-disks-from-honeybee-flight-muscle
#4
Mara Rusu, Zhongjun Hu, Kenneth A Taylor, John Trinick
The Z-disk is a complex structure comprising some 40 proteins that are involved in the transmission of force developed during muscle contraction and in important signalling pathways that govern muscle homeostasis. In the Z-disk the ends of antiparallel thin filaments from adjacent sarcomeres are crosslinked by α-actinin. The structure of the Z-disk lattice varies greatly throughout the animal kingdom. In vertebrates the thin filaments form a tetragonal lattice, whereas invertebrate flight muscle has a hexagonal lattice...
July 21, 2017: Journal of Muscle Research and Cell Motility
https://www.readbyqxmd.com/read/28732041/understanding-russell-s-viper-venom-factor-v-activator-s-substrate-specificity-by-surface-plasmon-resonance-and-in-silico-studies
#5
Pradeep K Yadav, Christian B Antonyraj, Syed Ibrahim Basheer Ahamed, Sistla Srinivas
Blood coagulation factor V (FV) is activated either by Factor X or thrombin, cleaving at three different sites viz., Site I (Arg709-Ser710), site II (Arg1018-Thr1019), and site III (Arg1545-Ser1546). Russell's viper venom factor V activator (RVV-V) is a thrombin-like serine proteinase that activates FV with selective, single cleavage at site III. A long lasting effort is being pending in understanding the 'selective' binding specificity of the RVV-V towards site III. Here, we present the binding kinetic study of RVV-V with two designed peptides corresponding to the regions from site I (Gln699-Asn713) and site II (1008Lys-Pro1022), respectively, that include 15 amino acids...
2017: PloS One
https://www.readbyqxmd.com/read/28729227/computational-and-experimental-prediction-of-molecules-involved-in-the-anti-melanoma-action-of-berberine
#6
Bin Liu, Xiu-Qiong Fu, Ting Li, Tao Su, Hui Guo, Pei-Li Zhu, Anfernee Kai-Wing Tse, Shi-Ming Liu, Zhi-Ling Yu
ETHNOPHARMACOLOGIC RELEVANCE: Berberine (BBR) is a naturally occurring alkaloid compound that can be found in Chinese medicinal herbs such as Rhizoma Coptidis and Phellodendri Cortex. These BBR containing herbs are commonly used by Chinese medicine doctors to treat cancers including melanoma. In this study, we explored proteins potentially involved in the anti-melanoma effects of BBR using an integrative computational and experimental approach. MATERIALS AND METHODS: Target proteins of BBR were predicted using the reverse pharmacophore screening, molecular docking and molecular dynamics...
July 17, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28728517/using-molecular-dynamics-for-the-refinement-of-atomistic-models-of-gpcrs-by-homology-modeling
#7
Cecylia S Lupala, Bahareh Rasaeifar, Patricia Gomez-Gutierrez, Juan J Perez
Despite GPCRs share a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs is steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modelling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28728041/multi-structure-docking-analysis-of-bace1-crystal-structures-and-non-peptidic-ligands
#8
Zahra Haghighijoo, Bahram Hemmateenejad, Najmeh Edraki, Ramin Miri, Saeed Emami
In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands' structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis...
June 28, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28726150/inhibition-mechanism-of-cdk-2-and-gsk-3%C3%AE-by-a-sulfamoylphenyl-derivative-of-indoline-a-molecular-dynamics-study
#9
Przemysław Czeleń
A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of such enzyme inhibition as analyzed by an indoline sulfamylophenyl derivative (CHEMBL410072). Previous work has shown that such compounds exhibit selective properties towards their biological targets...
August 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28725058/identification-of-a-flavonoid-glucosyltransferase-involved-in-7-oh-site-glycosylation-in-tea-plants-camellia-sinensis
#10
Xinlong Dai, Juhua Zhuang, Yingling Wu, Peiqiang Wang, Guifu Zhao, Yajun Liu, Xiaolan Jiang, Liping Gao, Tao Xia
Flavonol glycosides, which are often converted from aglycones in a process catalyzed by UDP-glycosyltransferases (UGTs), play an important role for the health of plants and animals. In the present study, a gene encoding a flavonoid 7-O-glycosyltransferase (CsUGT75L12) was identified in tea plants. Recombinant CsUGT75L12 protein displayed glycosyltransferase activity on the 7-OH position of multiple phenolic compounds. In relative comparison to wild-type seeds, the levels of flavonol-glucosides increased in Arabidopsis seeds overexpressing CsUGT75L12...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28725053/cyclic-di-gmp-regulates-mycobacterium-tuberculosis-resistance-to-ethionamide
#11
Hai-Nan Zhang, Zhao-Wei Xu, He-Wei Jiang, Fan-Lin Wu, Xiang He, Yin Liu, Shu-Juan Guo, Yang Li, Li-Jun Bi, Jiao-Yu Deng, Xian-En Zhang, Sheng-Ce Tao
Tuberculosis is still on the top of infectious diseases list on both mobility and mortality, especially due to drug-resistance of Mycobacterium tuberculosis (M.tb). Ethionamide (ETH) is one of effective second line anti-TB drugs, a synthetic compound similar to isoniazid (INH) structurally, with existing severe problem of ETH resistance. ETH is a prodrug, which is activated by Etha inside M.tb, and etha is transcriptionally repressed by Ethr. We found that c-di-GMP could bind Ethr, enhanced the binding of Ethr to the promoter of etha, and then repressed the transcription of etha, thus caused resistance of M...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724630/altered-met-receptor-phosphorylation-and-lrp1-mediated-uptake-in-cells-lacking-carbohydrate-dependent-lysosomal-targeting
#12
Megan Aarnio-Peterson, Peng Zhao, Seok-Ho Yu, Courtney Christian, Heather Flanagan-Steet, Lance Wells, Richard Steet
Acid hydrolases utilize a carbohydrate-dependent mechanism for lysosomal targeting. These hydrolases acquire a mannose 6-phosphate tag by the action of the GlcNAc-1-phosphotransferase enzyme, allowing them to bind receptors and traffic to endosomes. Loss of GlcNAc-1-phosphotransferase results in hydrolase hypersecretion and profound lysosomal storage. Little, however, is known about how these cellular phenotypes affect the trafficking, activity and localization of surface glycoproteins. To address this question, we profiled the abundance of surface glycoproteins in WT and CRISPR-mediated GNPTAB-/- HeLa cells and identified changes in numerous glycoproteins including the uptake receptor LRP1 and multiple receptor tyrosine kinases...
July 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28724188/bisindole-oxadiazole-hybrids-t3p-%C3%A2-mediated-synthesis-and-appraisal-of-their-apoptotic-antimetastatic-and-computational-bcl-2-binding-potential
#13
Pooja R Kamath, Manu M Joseph, Abdul Ajees Abdul Salam, Sreelekha T Therakathinal, Dhanya Sunil, Subhankar Biswas, Karkala Sreedhara Ranganath Pai
In the pursuit of novel anticancer leads, new bisindole-oxadiazoles were synthesized using propyl phosphonic anhydride as a mild and efficient reagent. The molecule, 3-[5-(1H-indol-3-ylmethyl)-1,3,4-oxadiazol-2-yl]-1H-indole (3a) exhibited selective cytotoxicity to MCF-7 cells with a cell cycle arrest in the G1 phase. The mechanism of cytotoxicity of 3a involved caspase-2-dependent apoptotic pathway with characteristic apoptotic morphological alterations as observed in acridine orange/ethidium bromide and Hoechst staining...
July 19, 2017: Journal of Biochemical and Molecular Toxicology
https://www.readbyqxmd.com/read/28723662/acetyl-lupeolic-acid-inhibits-akt-signaling-and-induces-apoptosis-in-chemoresistant-prostate-cancer-cells-in-vitro-and-in-vivo
#14
Claudia Schmidt, Cornelia Loos, Lu Jin, Michael Schmiech, Christoph Q Schmidt, Menna El Gaafary, Tatiana Syrovets, Thomas Simmet
The triterpenoid acetyl-lupeolic acid (ac-LA) isolated from the oleogum resin of Boswellia carterii reduced the viability of a panel of cancer cell lines more efficiently than lupeol. There was no detectable intracellular conversion of ac-LA to lupeol and vice versa. In contrast to docetaxel, ac-LA did not induce selection of treatment-resistant cancer cells. By various parameters including DNA fragmentation, ac-LA was shown to induce apoptosis in androgen-independent PC-3 cells, whereas in MDA-MB-231 breast cancer cells, ac-LA led to cell accumulation in the G2/M phase of the cell cycle, but not to apoptosis...
July 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28721542/molecular-characterization-modeling-in-silico-analysis-of-equine-pituitary-gonadotropin-alpha-subunit-and-docking-interaction-studies-with-ganirelix
#15
Anuradha Bhardwaj, Varij Nayan, Parvati Sharma, Sanjay Kumar, Yash Pal, Jitender Singh
Equine pituitary gonadotropins (eLH, eFSH, eCG) are heterodimeric glycoprotein hormones with alpha (α) and beta (β) subunits. It is responsible for maintenance of pregnancy in mares during early gestation and fairly valuable for inducing superovulation in animals other than equines. The alpha subunit is common, while beta subunit is species-specific in all glycoprotein hormones. In the present investigation, molecular cloning and in silico characterization including homology modeling and molecular docking analysis of the equine chorionic gonadotropin (eCG) alpha subunit was carried out for gaining structural and functional insights into the eCG alpha subunit and its possible interaction with ganirelix, a gonadotropin-releasing hormone (GnRH) antagonist...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28720969/quantification-of-phenolics-in-syzygium-cumini-seed-and-their-modulatory-role-on-tertiary-butyl-hydrogen-peroxide-induced-oxidative-stress-in-h9c2-cell-lines-and-key-enzymes-in-cardioprotection
#16
H P Syama, A D Arya, R Dhanya, P Nisha, A Sundaresan, E Jacob, P Jayamurthy
The study quantified the major phenolics in different fractions of Syzygium cumini seeds and evaluated their cardioprotective efficacy. Gallic acid, ellagic acid, cinnamic acid, quercetin, syringic acid and ferulic acid were the major polyphenols present in different fractions of Syzygium cumini seeds. The cardioprotective effect of Syzygium cumini seed fractions in modulating angiotensin converting enzyme (ACE), HMG-CoA reductase, LDL oxidation and tertiary butyl hydrogen peroxide (TBHP) induced oxidative stress in H9c2 cardiac cell lines were investigated...
June 2017: Journal of Food Science and Technology
https://www.readbyqxmd.com/read/28720769/concentration-dependent-binding-of-small-ligands-to-multiple-saturable-sites-in-membrane-proteins
#17
Letícia Stock, Juliana Hosoume, Werner Treptow
Membrane proteins are primary targets for most therapeutic indications in cancer and neurological diseases, binding over 50% of all known small molecule drugs. Understanding how such ligands impact membrane proteins requires knowledge on the molecular structure of ligand binding, a reasoning that has driven relentless efforts in drug discovery and translational research. Binding of small ligands appears however highly complex involving interaction to multiple transmembrane protein sites featuring single or multiple occupancy states...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720470/molecular-docking-prediction-and-in-vitro-studies-elucidate-anti-cancer-activity-of-phytoestrogens
#18
Shreelekha Dutta, Prashant S Kharkar, Niteshkumar U Sahu, Aparna Khanna
AIM: The study is aimed at evaluating the chemosensitization and apoptotic effect of aglycone rich extracts of dietary phytoestrogens (derived from soybean and flaxseed) on estrogen receptor positive, MCF-7 and estrogen receptor negative, MDA-MB-231 cells. The extracts show potent activity on both the cell lines, hence, in silico studies have been carried out to find the possible reason for their activity. MAIN METHODS: MTT assay was carried to assess chemosensitization effect and activated caspase-3/7 activity was studied using flow-cytometry and western blotting...
July 15, 2017: Life Sciences
https://www.readbyqxmd.com/read/28720122/enhance-the-performance-of-current-scoring-functions-with-the-aid-of-3d-protein-ligand-interaction-fingerprints
#19
Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li, Renxiao Wang
BACKGROUND: In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively...
July 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28719882/antileishmanial-activity-and-tubulin-polymerization-inhibition-of-podophyllotoxin-derivatives-on-leishmania-infantum
#20
José Miguel Escudero-Martínez, Yolanda Pérez-Pertejo, Rosa M Reguera, María Ángeles Castro, María Victoria Rojo, Carolina Santiago, Andrés Abad, Pablo Anselmo García, José Luis López-Pérez, Arturo San Feliciano, Rafael Balaña-Fouce
Leishmania microtubules play an important role not only in cell division, but also in keeping the shape of the parasite and motility of its free-living stages. Microtubules result from the self-assembly of alpha and beta tubulins, two phylogenetically conserved and very abundant eukaryotic proteins in kinetoplastids. The colchicine binding domain has inspired the discovery and development of several drugs currently in clinical use against parasites. However, this domain is less conserved in kinetoplastids and may be selectively targeted by new compounds...
June 28, 2017: International Journal for Parasitology, Drugs and Drug Resistance
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