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https://www.readbyqxmd.com/read/29334381/the-molecular-basis-of-subtype-selectivity-of-human-kinin-g-protein-coupled-receptors
#1
Lisa Joedicke, Jiafei Mao, Georg Kuenze, Christoph Reinhart, Tejaswi Kalavacherla, Hendrik R A Jonker, Christian Richter, Harald Schwalbe, Jens Meiler, Julia Preu, Hartmut Michel, Clemens Glaubitz
G-protein-coupled receptors (GPCRs) are the most important signal transducers in higher eukaryotes. Despite considerable progress, the molecular basis of subtype-specific ligand selectivity, especially for peptide receptors, remains unknown. Here, by integrating DNP-enhanced solid-state NMR spectroscopy with advanced molecular modeling and docking, the mechanism of the subtype selectivity of human bradykinin receptors for their peptide agonists has been resolved. The conserved middle segments of the bound peptides show distinct conformations that result in different presentations of their N and C termini toward their receptors...
January 15, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29333037/curcumin-and-natural-derivatives-inhibit-ebola-viral-proteins-an-in-silico-approach
#2
Shruti Baikerikar
Background: Ebola viral disease is a severe and mostly fatal disease in humans caused by Ebola virus. This virus belongs to family Filoviridae and is a single-stranded negative-sense virus. There is no single treatment for this disease which puts forth the need to identify new therapy to control and treat this fatal condition. Curcumin, one of the bioactives of turmeric, has proven antiviral property. Objective: The current study evaluates the inhibitory activity of curcumin, bisdemethoxycurcumin, demethoxycurcumin, and tetrahydrocurcumin against Zaire Ebola viral proteins (VPs)...
December 2017: Pharmacognosy Research
https://www.readbyqxmd.com/read/29332820/a-strategy-for-screening-of-%C3%AE-glucosidase-inhibitors-from-morus-alba-root-bark-based-on-the-ligand-fishing-combined-with-high-performance-liquid-chromatography-mass-spectrometer-and-molecular-docking
#3
Zhen Wang, Xiaoqing Li, Menghan Chen, Feiyan Liu, Chao Han, Lingyi Kong, Jianguang Luo
A new method based on ligand fishing combined with high-performance liquid chromatography quadrupole-time-of-flight mass spectrometer and molecular docking was established to screen α-glucosidase inhibitors from a traditional Chinese medicine Morus alba root bark. α-Glucosidase was immobilized on magnetic nanoparticles, used as a solid support to incubate with crude extract. After ligand fishing, the eluates were analyzed by high-performance liquid chromatography quadrupole-time-of-flight mass spectrometer, obtaining eleven ligands (1-4, 6-12) eventually...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29332600/finding-novel-anti-carcinomas-compounds-by-targeting-sfrp4-through-molecular-modeling-docking-and-dynamic-simulation-studies
#4
M Hassan, M Azhar, Q Abbas, H Reza, A A Moustafa, S Shahzadi, Z Ashraf, S Y Seo
BACKGROUND: Secreted frizzled-related protein 4 (SFRP4) is a glycoprotein that act as a competitor of both canonical and non-canonical Wnt pathways. SFRP4 is mostly expressed in ovary and played a significant role as a target molecule to cure ovarian carcinoma. OBJECTIVE: Multiple chemical agonists are being used to cure ovary melanoma. We are interested to theoretically analyze the compounds through computational approaches for their inhibitory effects against SFRP4...
January 11, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29332299/similarity-search-combined-with-docking-and-molecular-dynamics-for-novel-hache-inhibitor-scaffolds
#5
Nadia Melo Borges, Geraldo Rodrigues Sartori, Jean F R Ribeiro, Josmar R Rocha, João B L Martins, Carlos A Montanari, Ricardo Gargano
The main purpose of this study was to address the performance of virtual screening methods based on ligands and the protein structure of acetylcholinesterase (AChE) in order to retrieve novel human AChE (hAChE) inhibitors. In addition, a protocol was developed to identify novel hit compounds and propose new promising AChE inhibitors from the ZINC database with 10 million commercially available compounds. In this sense, 3D similarity searches using rapid overlay of chemical structures and similarity analysis through comparison of electrostatic overlay of docked hits were used to retrieve AChE inhibitors from collected databases...
January 13, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29331879/structural-and-quantum-mechanical-computations-to-elucidate-the-altered-binding-mechanism-of-metal-and-drug-with-pyrazinamidase-from-mycobacterium-tuberculosis-due-to-mutagenicity
#6
Nouman Rasool, Saima Iftikhar, Anam Amir, Waqar Hussain
Pyrazinamide is known to be the most effective treatment against tuberculosis disease and is known to have bacteriostatic action. By targeting the bacterial spores, this drug reduces the chances for the progression of the infection in organisms. In recent years, increased instances of the drug resistance of bacterial strains are reported. Pyrazinamidase, activator for pyrazinamide, leads to resistance against the drug due to mutagenicity across the world. The present study aimed at the quantum mechanistic analysis of mutations in pyrazinamidase to gain insights into the mechanism of this enzyme...
December 24, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29330887/loss-of-vamp5-in-mice-results-in-duplication-of-the-ureter-and-insufficient-expansion-of-the-lung
#7
Maiko Ikezawa, Yuki Tajika, Hitoshi Ueno, Tohru Murakami, Naokazu Inoue, Hiroshi Yorifuji
BACKGROUND: VAMP5 is a member of the SNARE protein family, which regulate the docking and fusion of membrane vesicles within cells. Previously, we reported ubiquitous expression of VAMP5 proteins in various organs except the brain and small intestine. However, the precise roles of VAMP5 in each organ remain unclear. To explore the roles of VAMP5 in vivo, we generated VAMP5 knockout (KO) mice. RESULTS: VAMP5 KO mice showed low birth rate and low body weight. KO embryos grew normally in the uterus, and tended to die around birth...
January 13, 2018: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/29330385/docking-thermodynamics-and-molecular-dynamics-md-studies-of-a-non-canonical-protease-inhibitor-mp-4-from-mucuna-pruriens
#8
Ashish Kumar, Harmeet Kaur, Abha Jain, Deepak T Nair, Dinakar M Salunke
Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329815/exploring-molecular-insights-into-the-interaction-mechanism-of-cholesterol-derivatives-with-the-mce4a-a-combined-spectroscopic-and-molecular-dynamic-simulation-studies
#9
Shagufta Khan, Faez Iqbal Khan, Taj Mohammad, Parvez Khan, Gulam Mustafa Hasan, Kevin A Lobb, Asimul Islam, Faizan Ahmad, Md Imtaiyaz Hassan
Mammalian cell entry protein (Mce4A) is a member of MCE-family, and is being considered as a potential drug target of Mycobacterium tuberculosis infection because it is required for invasion and latent survival of pathogen by utilizing host's cholesterol. In the present study, we performed molecular docking followed by 100 ns MD simulation studies to understand the mechanism of interaction of Mce4A to the cholesterol derivatives and probucol. The selected ligands, cholesterol, 25-hydroxycholesterol, 5-cholesten-3β-ol-7-one and probucol bind to the predicted active site cavity of Mce4A, and complexes remain stable during entire simulation of 100 ns...
January 9, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29329283/modeling-the-assembly-order-of-multimeric-heteroprotein-complexes
#10
Lenna X Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly...
January 12, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29327289/study-of-adenylyl-cyclase-g%C3%AE-s-interactions-and-identification-of-novel-ac-ligands
#11
Appalaraju Jaggupilli, Premnath Dhanaraj, Alexander Pritchard, John L Sorensen, Shyamala Dakshinamurti, Prashen Chelikani
Adenylyl cyclases (ACs) are membrane bound enzymes that catalyze the production of cAMP from ATP in response to the activation by G-protein Gαs. Different isoforms of ACs are ubiquitously expressed in different tissues involved in regulatory mechanisms in response to specific stimulants. There are 9 AC isoforms present in humans, with AC5 and AC6 proposed to play a vital role in cardiac functions. The activity of AC6 is sensitive to nitric oxide, such that nitrosylation of the protein might regulate its function...
January 11, 2018: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29327005/vivo-complexes-with-antibacterial-quinolone-ligands-and-their-interaction-with-serum-proteins
#12
Daniele Sanna, Valeria Ugone, Giuseppe Sciortino, Péter Buglyó, Zsolt Bihari, Péter László Parajdi-Losonczi, Eugenio Garribba
Quinolone derivatives are among the most commonly prescribed antibacterials in the world and could also attract interest as organic ligands in the design of metal complexes with potential pharmacological activity. In this study, five compounds, belonging to the first (nalidixic acid or Hnal), second (ciprofloxacin or Hcip, and norfloxacin or Hnor) and third generation (levofloxacin or Hlev, and sparfloxacin or Hspar) of quinolones, were used as ligands to bind the VIVO2+ ion. In aqueous solution, mono- and bis-chelated species were formed as a function of pH, with cis-[VOHxL2(H2O)]x+ and [VOHxL2]x+, x = 0-2, being the major complexes at pH 7...
January 12, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29326881/interaction-of-anthraquinones-of-cassia-occidentalis-seeds-with-dna-and-glutathione
#13
Gati Krushna Panigrahi, Neeraj Verma, Nivedita Singh, Somya Asthana, Shailendra K Gupta, Anurag Tripathi, Mukul Das
Consumption of Cassia occidentalis (CO) seeds has been associated with the hepatomyoencephalopathy (HME) in children. Recently, we have characterized the toxic anthraquinones (AQs) such as Emodin, Rhein, Aloe-emodin, Chrysophanol and Physcion in CO seeds and detected these moieties in the bio fluids of CO poisoning cases. As AQs were detected in the serum of HME patients, their interaction with key biomolecules including protein, DNA and glutathione (GSH) is imperative. In this regard, we have previously reported the interaction of these AQs with serum albumin protein and their subsequent biological effects...
2018: Toxicology Reports
https://www.readbyqxmd.com/read/29326158/reciprocal-spatiotemporally-controlled-apoptosis-regulates-wolffian-duct-cloaca-fusion
#14
Masato Hoshi, Antoine Reginensi, Matthew S Joens, James A J Fitzpatrick, Helen McNeill, Sanjay Jain
The epithelial Wolffian duct (WD) inserts into the cloaca (primitive bladder) before metanephric kidney development, thereby establishing the initial plumbing for eventual joining of the ureters and bladder. Defects in this process cause common anomalies in the spectrum of congenital anomalies of the kidney and urinary tract (CAKUT). However, developmental, cellular, and molecular mechanisms of WD-cloaca fusion are poorly understood. Through systematic analysis of early WD tip development in mice, we discovered that a novel process of spatiotemporally regulated apoptosis in WD and cloaca was necessary for WD-cloaca fusion...
January 11, 2018: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29325877/dmcatd-a-cathepsin-d-like-peptidase-of-the-hematophagous-insect-dipetalogaster-maxima-hemiptera-reduviidae-purification-bioinformatic-analyses-and-the-significance-of-its-interaction-with-lipophorin-in-the-internalization-by-developing-oocytes
#15
Jimena Leyria, Leonardo L Fruttero, Rodrigo Ligabue-Braun, Marina S Defferrari, Estela L Arrese, José L Soulages, Beatriz P Settembrini, Celia R Carlini, Lilián E Canavoso
DmCatD, a cathepsin D-like peptidase of the hematophagous insect Dipetalogaster maxima, is synthesized by the fat body and the ovary and functions as yolk protein precursor. Functionally, DmCatD is involved in vitellin proteolysis. In this work, we purified and sequenced DmCatD, performed bioinformatic analyses and investigated the events involved in its targeting and storage in developing oocytes. By ion exchange and gel filtration chromatography, DmCatD was purified from egg homogenates and its identity was confirmed by mass spectrometry...
January 8, 2018: Journal of Insect Physiology
https://www.readbyqxmd.com/read/29324789/an-l213a-variant-of-%C3%AE-glycosidase-from-sulfolobus-solfataricus-with-increased-%C3%AE-l-arabinofuranosidase-activity-converts-ginsenoside-rc-to-compound-k
#16
Ji-Hyeon Choi, Kyung-Chul Shin, Deok-Kun Oh
Compound K (C-K) is a crucial pharmaceutical and cosmetic component because of disease prevention and skin anti-aging effects. For industrial application of this active compound, the protopanaxadiol (PPD)-type ginsenosides should be transformed to C-K. β-Glycosidase from Sulfolobus solfataricus has been reported as an efficient C-K-producing enzyme, using glycosylated PPD-type ginsenosides as substrates. β-Glycosidase from S. solfataricus can hydrolyze β-d-glucopyranoside in ginsenosides Rc, C-Mc1, and C-Mc, but not α-l-arabinofuranoside in these ginsenosides...
2018: PloS One
https://www.readbyqxmd.com/read/29324718/screening-of-e-coli-%C3%AE-clamp-inhibitors-revealed-that-few-inhibit-helicobacter-pylori-more-effectively-structural-and-functional-characterization
#17
Preeti Pandey, Vijay Verma, Suman Kumar Dhar, Samudrala Gourinath
The characteristic of interaction with various enzymes and processivity-promoting nature during DNA replication makes β-clamp an important drug target. Helicobacter pylori (H. pylori) have several unique features in DNA replication machinery that makes it different from other microorganisms. To find out whether difference in DNA replication proteins behavior accounts for any difference in drug response when compared to E. coli, in the present study, we have tested E. coli β-clamp inhibitor molecules against H...
January 11, 2018: Antibiotics
https://www.readbyqxmd.com/read/29322920/investigation-and-identification-of-functional-post-translational-modification-sites-associated-with-drug-binding-and-protein-protein-interactions
#18
Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee
BACKGROUND: Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322818/evolution-of-ph-buffers-and-water-homeostasis-in-eukaryotes-homology-between-humans-and-acanthamoeba-proteins
#19
Abdul M Baig, R Zohaib, S Tariq, H R Ahmad
AIM: This study intended to trace the evolution of acid-base buffers and water homeostasis in eukaryotes. Acanthamoeba castellanii  was selected as a model unicellular eukaryote for this purpose. Homologies of proteins involved in pH and water regulatory mechanisms at cellular levels were compared between humans and A. castellanii. MATERIALS & METHODS: Amino acid sequence homology, structural homology, 3D modeling and docking prediction were done to show the extent of similarities between carbonic anhydrase 1 (CA1), aquaporin (AQP), band-3 protein and H+ pump...
January 11, 2018: Future Microbiology
https://www.readbyqxmd.com/read/29321504/structural-ensemble-based-docking-simulation-and-biophysical-studies-discovered-new-inhibitors-of-hsp90-n-terminal-domain
#20
Hyun-Hwi Kim, Ja-Shil Hyun, Joonhyeok Choi, Kwang-Eun Choi, Jun-Goo Jee, Sung Jean Park
Heat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and plays a substantial role in the folding of client proteins. The inhibition of Hsp90 has been regarded as an attractive therapeutic strategy for treating cancer because many oncogenic kinases are Hsp90 client proteins. In this study, we report new inhibitors that directly bind to N-terminal ATP-binding pocket of Hsp90. Optimized structure-based virtual screening predicted candidate molecules, which was followed by confirmation using biophysical and cell-based assays...
January 10, 2018: Scientific Reports
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