keyword
MENU ▼
Read by QxMD icon Read
search

Docking

keyword
https://www.readbyqxmd.com/read/29149726/protein-structure-based-drug-design-from-docking-to-molecular-dynamics
#1
REVIEW
Paweł Śledź, Amedeo Caflisch
Recent years have witnessed rapid developments of computer-aided drug design methods, which have reached accuracy that allows their routine practical applications in drug discovery campaigns. Protein structure-based methods are useful for the prediction of binding modes of small molecules and their relative affinity. The high-throughput docking of up to 10(6) small molecules followed by scoring based on implicit-solvent force field can robustly identify micromolar binders using a rigid protein target. Molecular dynamics with explicit solvent is a low-throughput technique for the characterization of flexible binding sites and accurate evaluation of binding pathways, kinetics, and thermodynamics...
November 14, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29149637/antiviral-potential-of-natural-compounds-against-influenza-virus-hemagglutinin
#2
S Kannan, P Kolandaivel
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29148766/heterodimeric-diterpenoids-isolated-from-euphorbia-ebracteolata-roots-and-their-inhibitory-effects-on-%C3%AE-glucosidase
#3
Yunlong Wei, Chao Wang, Zhongbin Cheng, Xiangge Tian, Jingming Jia, Yonglei Cui, Lei Feng, Chengpeng Sun, Baojing Zhang, Xiaochi Ma
Two heterodimeric diterpenoids (1 and 2) comprising abietane lactone and nor-rosane constituent units were isolated from Euphorbia ebracteolata roots. Compound 1 exhibited a moderate inhibitory effect on α-glucosidase (IC50 = 7.94 μM), with a Ki value of 10.8 μM. In silico molecular docking has been performed to investigate the inhibition mechanism. Compound 2 inhibited the acetyl transfer activity of Mycobacterium tuberculosis GlmU (IC50 = 41.85 μM), which is a novel tuberculosis treatment target.
November 17, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/29147652/identification-of-potent-chloride-intracellular-channel-protein-1-inhibitors-from-traditional-chinese-medicine-through-structure-based-virtual-screening-and-molecular-dynamics-analysis
#4
Wei Wang, Minghui Wan, Dongjiang Liao, Guilin Peng, Xin Xu, Weiqiang Yin, Guixin Guo, Funeng Jiang, Weide Zhong, Jianxing He
Chloride intracellular channel 1 (CLIC1) is involved in the development of most aggressive human tumors, including gastric, colon, lung, liver, and glioblastoma cancers. It has become an attractive new therapeutic target for several types of cancer. In this work, we aim to identify natural products as potent CLIC1 inhibitors from Traditional Chinese Medicine (TCM) database using structure-based virtual screening and molecular dynamics (MD) simulation. First, structure-based docking was employed to screen the refined TCM database and the top 500 TCM compounds were obtained and reranked by X-Score...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29147015/structure-of-flgk-reveals-the-divergence-of-the-bacterial-hook-filament-junction-of-campylobacter
#5
Paula V Bulieris, Nausad H Shaikh, Peter L Freddolino, Fadel A Samatey
Evolution of a nano-machine consisting of multiple parts, each with a specific function, is a complex process. A change in one part should eventually result in changes in other parts, if the overall function is to be conserved. In bacterial flagella, the filament and the hook have distinct functions and their respective proteins, FliC and FlgE, have different three-dimensional structures. The filament functions as a helical propeller and the hook as a flexible universal joint. Two proteins, FlgK and FlgL, assure a smooth connectivity between the hook and the filament...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29147012/piperidylmethyloxychalcone-improves-immune-mediated-acute-liver-failure-via-inhibiting-tak1-activity
#6
Sun Hong Park, Jeong-Ah Kwak, Sang-Hun Jung, Byeongwoo Ahn, Won-Jea Cho, Cheong-Yong Yun, Chang Seon Na, Bang Yeon Hwang, Jin Tae Hong, Sang-Bae Han, Youngsoo Kim
Mice deficient in the toll-like receptor (TLR) or the myeloid differentiation factor 88 (MyD88) are resistant to acute liver failure (ALF) with sudden death of hepatocytes. Chalcone derivatives from medicinal plants protect from hepatic damages including ALF, but their mechanisms remain to be clarified. Here, we focused on molecular basis of piperidylmethyloxychalcone (PMOC) in the treatment of TLR/MyD88-associated ALF. C57BL/6J mice were sensitized with D-galactosamine (GalN) and challenged with Escherichia coli lipopolysaccharide (LPS, TLR4 agonist) or oligodeoxynucleotide containing unmethylated CpG motif (CpG ODN, TLR9 agonist) for induction of ALF...
November 17, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29146871/postcatalytic-spliceosome-structure-reveals-mechanism-of-3-splice-site-selection
#7
Max E Wilkinson, Sebastian M Fica, Wojciech P Galej, Christine M Norman, Andrew J Newman, Kiyoshi Nagai
Introns are removed from eukaryotic mRNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7Å cryo-EM structure of the yeast P complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5'-splice site and the branch point adenosine. After the branching reaction protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29146452/design-synthesis-and-biological-evaluation-of-thieno-2-3-d-pyrimidine-derivatives-as-novel-dual-c-met-and-vegfr-2-kinase-inhibitors
#8
Jieming Li, Weijie Gu, Xinzhou Bi, Huilan Li, Chen Liao, Chunxia Liu, Wenlong Huang, Hai Qian
Both c-Met and VEGFR-2 are important targets for cancer therapies. Here we report a series of potent dual c-Met and VEGFR-2 inhibitors bearing thieno[2,3-d]pyrimidine scaffold. The cell proliferation assay in vitro demonstrated that most target compounds had inhibition potency both on c-Met and VEGFR-2 with IC50 values in nanomolar range, especially compound 12j and 12m. Based on the further enzyme assay in vitro, compound 12j was considered as the most potent one, the IC50 values of which were 25 nM and 48 nM for c-Met and VEGFR-2, respectively...
November 4, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29146372/interactions-of-cinnamaldehyde-and-its-metabolite-cinnamic-acid-with-human-serum-albumin-and-interference-of-other-food-additives
#9
Qiaomei Sun, Hongqin Yang, Peixiao Tang, Jiuyang Liu, Wan Wang, Hui Li
Considering the adverse effect of food additives on humans, thorough research of their physiological effects at the molecular level is important. The interactions of cinnamaldehyde (CNMA), a food perfume, and its major metabolite cinnamic acid (CA) with human serum albumin (HSA) were examined by multiple-spectroscopies. NMR analysis revealed CNMA and CA both bound to HSA, and STD-NMR experiments established CNMA and CA primarily interacted with site I and site II of HSA, respectively. The ligands caused strong quenching of HSA fluorescence through a static quenching mechanism, with hydrophobic and electrostatic interaction between CNMA/CA and HSA, respectively...
March 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29146317/characterization-of-binding-interactions-between-selected-phenylpropanoid-glycosides-and-trypsin
#10
Yue Feng, Moyang Lv, YuQin Lu, Ke Liu, Lizhong Liu, Zhendan He, Kaimin Wu, Xinrong Wang, Baoshuang Zhang, Xuli Wu
Phenylpropanoid glycosides (PPGs) are important bioactive polyphenolic compounds that are widely distributed in plants. In this paper, the inhibitory effects of four selected PPGs against trypsin were investigated. The interactions between these PPGs and trypsin were further investigated by multiple spectroscopic methods and molecular docking studies. The results showed that the binding of each of these PPGs to trypsin induced changes in the natural conformation of trypsin, which inhibited the enzyme in the following order: acteoside>syringalide A 3'-α-l-rhamnopyranoside>lipedoside A-I>osmanthuside B...
March 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29146198/bisphenol-a-alternatives-bisphenol-s-and-bisphenol-f-interfere-with-thyroid-hormone-signaling-pathway-in%C3%A2-vitro-and-in%C3%A2-vivo
#11
Yin-Feng Zhang, Xiao-Min Ren, Yuan-Yuan Li, Xiao-Fang Yao, Chuan-Hai Li, Zhan-Fen Qin, Liang-Hong Guo
The wide use of the alternatives to bisphenol A (BPA) has raised concerns about their potential toxicities. Considering the disrupting activity of BPA on thyroid hormone (TH) signaling, we investigated whether bisphenol S (BPS) and bisphenol F (BPF), two leading alternatives, could interfere with TH signaling pathway using a series of assays in vitro and in vivo. In the fluorescence competitive binding assay, we found BPS and BPF, like BPA, bound to TH receptors (TRα and TRβ), with the binding potencies an order of magnitude lower than BPA (BPA > BPF > BPS)...
November 13, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29146161/intraoperative-workflow-for-all-inside-anterior-cruciate-ligament-reconstruction-an-in%C3%A2-vitro-biomechanical-evaluation-of-preconditioning-and-knot-tying
#12
Edoardo Monaco, Samuel Bachmaier, Mattia Fabbri, Riccardo Maria Lanzetti, Coen A Wijdicks, Andrea Ferretti
PURPOSE: To evaluate and compare the effect of preconditioning according to intraoperative workflow on the elongation behavior of single-side and fully knotted all-inside anterior cruciate ligament (ACL) reconstruction configurations in a biomechanical in vitro study. METHODS: Four full construct all-inside ACL reconstruction groups (n = 8 per group) were tested using porcine tibias and bovine tendons. Groups included both an all-inside configuration with one- (group 1) and both-side knotted adjustable loop-length devices (group 2), without and with performing intraoperative preconditioning (group 1-intraoperative preconditioned [IPC], group 2-IPC)...
November 13, 2017: Arthroscopy: the Journal of Arthroscopic & related Surgery
https://www.readbyqxmd.com/read/29145791/impact-of-novel-n-aryl-piperamide-no-donors-on-nf-%C3%AE%C2%BAb-translocation-in-neuroinflammation-rational-drug-designing-synthesis-and-biological-evaluation
#13
Sajad Shahbazi, Jagdeep Kaur, Shikha Singh, K Gopinath Achary, Sameena Wani, Sobhagyalaxmi Jema, Jabed Akhtar, Ranbir Chander Sobti
NO donor drugs showed a significant therapeutic effect in the treatment of many diseases, such as arteriopathies, various acute and chronic inflammatory conditions, and several degenerative diseases. NO-releasing anti-inflammatory drugs are the prototypes of a novel class of compounds, combining the pharmacological activities of anti-inflammatory and anti-nociceptive of drugs with those of NO, thus possessing potential therapeutic applications in a great variety of diseases. In this study, we designed and predicted biological activity by targeting cyclooxygenase type 2 (COX-2) and NF-κB subunits and pharmacological profiling along with toxicity predictions of various N-aryl piperamides linked via an ester bond to a spacer that is bound to a NO-releasing moiety (-ONO2)...
January 1, 2017: Innate Immunity
https://www.readbyqxmd.com/read/29145059/binding-of-naringin-and-naringenin-with-hen-egg-white-lysozyme-a-spectroscopic-investigation-and-molecular-docking-study
#14
Sourav Das, Pooja Ghosh, Sudipta Koley, Atanu Singha Roy
The interactions of naringenin (NG) and naringin (NR) with Hen Egg White Lysozyme (HEWL) in aqueous medium have been investigated using UV-vis spectroscopy, steady-state fluorescence, circular dichroism (CD), Fourier Transform infrared spectroscopy (FT-IR) and molecular docking analyses. Both NG and NR can quench the intrinsic fluorescence of HEWL via static quenching mechanism. At 300K, the value of binding constant (Kb) of HEWL-NG complex (5.596±0.063×10(4)M(-1)) was found to be greater than that of HEWL-NR complex (3...
November 8, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29145034/molecular-insight-into-mutation-induced-conformational-change-in-metastasic-bowel-cancer-braf-kinase-domain-and-its-implications-for-selective-inhibitor-design
#15
Kai Zhao, Xin Zhou, Ming Ding
Oncogenic BRAF V600E mutation confers constitutive activation for the kinase and is closely related to the pathogenesis of metastasic bowel cancer (MBC). Here, the V600E-induced conformational change in MBC BRAF kinase domain is characterized systematically at structural, energetic and dynamic levels. The mutation is observed to cause a conformational conversion of the kinase's activation loop from DFG-out to DFG-in, thus activating the kinase. Electrostatic force is primarily responsible for the conformational conversion and stabilization of DFG-in associated with the mutation...
November 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29144748/chemical-modification-for-proteolytic-stabilization-of-the-selective-%C3%AE-v%C3%AE-3-integrin-rgdechi-peptide-in-vitro-and-in-vivo-activities-on-malignant-melanoma-cells
#16
Daniela Comegna, Antonella Zannetti, Annarita Del Gatto, Ivan de Paola, Luigi Russo, Sonia Di Gaetano, Annamaria Liguoro, Domenica Capasso, Michele Saviano, Laura Zaccaro
Herein we report the synthesis and biological characterization of the novel peptide ψRGDechi as the first step towards novel targeted theranostics in melanoma. This pseudo-peptide is designed from our previously reported RGDechi peptide, known to bind selectively αvβ3 integrin, and differs for a modified amide bond at the main protease cleavage site. This chemical modification drastically reduces the enzymatic degradation in serum, compared to its parental peptide, resulting in an overall magnification of the biological activity on a highly expressing αvβ3 human metastatic melanoma cell line...
November 16, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29144001/biological-evaluation-and-energetic-analyses-of-novel-gsk-3%C3%AE-inhibitors
#17
Denan Zhang, Lei Liu, Lin Pang, Qing Jin, Kehui Ke, Ming Hu, Jingbo Yang, Weifang Ma, Hongbo Xie, Xiujie Chen
Glycogen synthase kinase-3 beta (GSK-3β) is involved in multiple signaling pathways. Consistent with its critical roles in normal cells, abnormalities in GSK-3β activity have been implicated in diabetes, heart disease, Parkinson disease and Alzheimer's disease. In this study, a series of new scaffolds of small molecule inhibitors of GSK-3β were identified by virtual screening and bioassay. Candidates that adhere to drug-like criteria from a virtual library of compounds were tested using computational docking studies...
November 16, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29143485/synthesis-molecular-modeling-and-biological-evaluation-of-4-5-aryl-3-thiophen-2-yl-4-5-dihydro-1h-pyrazol-1-yl-benzenesulfonamides-towards-acetylcholinesterase-carbonic-anhydrase-i-and-ii-enzymes
#18
Cem Yamali, Halise Inci Gul, Abdulilah Ece, Parham Taslimi, Ilhami Gulcin
In the present study, 4-[5-aryl-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazol-1-yl] benzenesulfonamides were synthesized and inhibition effects on AChE, hCA I and hCA II were evaluated. Ki values of the compounds towards hCA I were in the range of 24.2±4.6-49.8±12.8 nM while they were in the range of 37.3±9.0-65.3±16.7 nM towards hCA II. Ki values of the Acetazolamide were 282.1±19.7 nM and 103.60±27.6 nM towards both isoenzymes, respectively. The compounds inhibited AChE with Ki in the range of 22.7±10.3-109...
November 16, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29142438/molecular-simulation-based-combinatorial-modeling-and-antioxidant-activities-of-zingiberaceae-family-rhizomes
#19
Talambedu Usha, Sushen Pradhan, Arvind Kumar Goyal, Shanmugarajan Dhivya, H P Prashanth Kumar, Manoj Kumar Singh, Neelu Joshi, Bharat Chandra Basistha, K R Siddalinga Murthy, Saravanakumar Selvaraj, Sushil Kumar Middha
Objective: The main aim of this scientific report was to investigate a series of phytochemicals in silico and the pharmacology of four plants found at higher altitude in the ginger family, Zingiberaceae (incl. Costaceae) from North-East India, particularly Sikkim. First, the goal was to determine the biological activities of the four herbs (used under Zingiberaceae family) using antioxidant assays to identify the best species. Second, previously reported compounds in litero were subsequently screened for their anticancerous activities using in silico methods...
October 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/29142437/docking-based-screening-of-ficus-religiosa-phytochemicals-as-inhibitors-of-human-histamine-h2-receptor
#20
Amit Chaudhary, Birendra Singh Yadav, Swati Singh, Pramod Kumar Maurya, Alok Mishra, Shweta Srivastva, Pritish Kumar Varadwaj, Nand Kumar Singh, Ashutosh Mani
Background: Ficus religiosa L. is generally known as Peepal and belongs to family Moraceae. The tree is a source of many compounds having high medicinal value. In gastrointestinal tract, histamine H2 receptors have key role in histamine-stimulated gastric acid secretion. Their over stimulation causes its excessive production which is responsible for gastric ulcer. Objective: This study aims to screen the range of phytochemicals present in F. religiosa for binding with human histamine H2 and identify therapeutics for a gastric ulcer from the plant...
October 2017: Pharmacognosy Magazine
keyword
keyword
84854
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"