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https://www.readbyqxmd.com/read/27933733/mannich-bases-of-1-2-4-triazole-3-thione-containing-adamantane-moiety-synthesis-preliminary-anticancer-evaluation-and-molecular-modeling-studies
#1
Milorad Z Milošev, Katarina Jakovljević, Milan D Joksović, Tatjana Stanojković, Ivana Z Matić, Milka Perović, Vesna Tešić, Selma Kanazir, Milan Mladenović, Marko V Rodić, Vukadin M Leovac, Snežana Trifunović, Violeta Marković
A series of 18 novel N-Mannich bases derived from 5-adamantyl-1,2,4-triazole-3-thione was synthesized and characterized using NMR spectroscopy and X-ray diffraction technique. All derivatives were evaluated for their anticancer potential against four human cancer cell lines. Several tested compounds exerted good cytotoxic activities on K562 and HL-60 cell lines, along with pronounced selectivity, showing lower cytotoxicity against normal fibroblasts MRC-5 compared to cancer cells. The effects of compounds 5b, 5e and 5j on the cell cycle were investigated by flow cytometric analysis...
December 9, 2016: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/27933673/a-biophysical-and-computational-study-unraveling-the-molecular-interaction-mechanism-of-a-new-janus-kinase-inhibitor-tofacitinib-with-bovine-serum-albumin
#2
Ali Saber Abdelhameed, Saima Nusrat, Mohammad Rehan Ajmal, Syed Mohammad Zakariya, Masihuz Zaman, Rizwan Hasan Khan
The interaction of a recently certified kinase inhibitor Tofacitinib (TFB) with bovine serum albumin (BSA) has been studied, by spectroscopic and molecular docking studies. Spectrofluorimetric measurements at 3 different temperatures (288, 298, and 310 K) showed that TFB quench the intrinsic fluorescence of BSA upon forming a nonfluorescent complex. The intrinsic fluorescence data showed that TFB binds to BSA with binding constant (Kb ) of approximately 10(4) M(-1) , affirming a significant affinity of TFB with BSA...
December 9, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27933426/characterization-of-the-first-fully-human-anti-tem1-scfv-in-models-of-solid-tumor-imaging-and-immunotoxin-based-therapy
#3
Xiaopeng Yuan, Mingjuan Yang, Xiang Chen, Xuhua Zhang, Shrey Sukhadia, Najia Musolino, Huijing Bao, Tingtao Chen, Chen Xu, Qirui Wang, Stephen Santoro, Daniel Ricklin, Jia Hu, Ruihe Lin, Wei Yang, Zhijun Li, Weijun Qin, Aizhi Zhao
Tumor endothelial marker 1 (TEM1) has been identified as a novel surface marker upregulated on the blood vessels and stroma in many solid tumors. We previously isolated a novel single-chain variable fragment (scFv) 78 against TEM1 from a yeast display scFv library. Here, we evaluated the potential applications of scFv78 as a tool for tumor molecular imaging, immunotoxin-based therapy and nanotherapy. Epitope mapping, three-dimensional structure docking and affinity measurements indicated that scFv78 could bind to both human and murine TEM1, with equivalent affinity, at a well-conserved conformational epitope...
December 8, 2016: Cancer Immunology, Immunotherapy: CII
https://www.readbyqxmd.com/read/27932949/muscle-type-nicotinic-receptor-modulation-by-2-6-dimethylaniline-a-molecule-resembling-the-hydrophobic-moiety-of-lidocaine
#4
Armando Alberola-Die, Gregorio Fernández-Ballester, José M González-Ros, Isabel Ivorra, Andrés Morales
To identify the molecular determinants responsible for lidocaine blockade of muscle-type nAChRs, we have studied the effects on this receptor of 2,6-dimethylaniline (DMA), which resembles lidocaine's hydrophobic moiety. Torpedo marmorata nAChRs were microtransplanted to Xenopus oocytes and currents elicited by ACh (IACh), either alone or co-applied with DMA, were recorded. DMA reversibly blocked IACh and, similarly to lidocaine, exerted a closed-channel blockade, as evidenced by the enhancement of IACh blockade when DMA was pre-applied before its co-application with ACh, and hastened IACh decay...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27931154/inhibition-of-ikk%C3%AE-by-celastrol-and-its-analogues-an-in-silico-and-in-vitro-approach
#5
Karpagam Veerappan, Sathishkumar Natarajan, Purushoth Ethiraj, Umashankar Vetrivel, Shila Samuel
CONTEXT: Alzheimer's disease (AD) is the most common form of dementia affecting the aged population and neuroinflammation is one of the most observed AD pathologies. NF-κB is the central regulator of inflammation and inhibitor κB kinase (IKK) is the converging point in NF-κB activation. Celastrol is a natural triterpene used as a treatment for inflammatory conditions. OBJECTIVE: This study determines the neuroprotective and inhibitory effect of celastrol on amyloid beta1-42 (Aβ1-42) induced cytotoxicity and IKKβ activity, respectively...
December 2017: Pharmaceutical Biology
https://www.readbyqxmd.com/read/27929168/a-computational-study-of-self-assembled-hexapeptide-inhibitors-against-amyloid-%C3%AE-a%C3%AE-aggregation
#6
Yuan Qiao, Mingzhen Zhang, Ya'nan Liang, Jie Zheng, Guizhao Liang
The fibrillation and deposition of amyloid-β (Aβ) peptides in human brains are pathologically linked to Alzheimer's disease (AD). Development of different inhibitors (peptides, organic molecules, and nanoparticles) to prevent Aβ aggregation becomes a promising therapeutic strategy for AD treatment. We recently propose a "like-interacts-like" design principle to computationally design/screen and experimentally validate a new set of hexapeptide inhibitors with completely different sequences from the Aβ sequence...
December 8, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27929054/in-silico-identification-of-snp-diversity-in-cultivated-and-wild-tomato-species-insight-from-molecular-simulations
#7
Archana Bhardwaj, Yogeshwar Vikram Dhar, Mehar Hasan Asif, Sumit K Bag
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928960/research-advances-in-molecular-modeling-in-cyclodextrins
#8
Qianqian Zhao, Weixiang Zhang, Runmiao Wang, Yitao Wang, Defang Ouyang
BACKGROUND: Cyclodextrins (CDs), as one type of the novel pharmaceutical excipients, have been widely used in drug delivery and pharmaceutical industry. Over the past decades, a large amount of molecular modeling studies in CDs were reported for profound understanding of structural, dynamic and energetic features of CDs systems. Thus, this review is focused on qualitative and quantitative analysis of research outputs on molecular modeling in CDs. METHODS: The original data were collected from Web of Science and analyzed by scientific knowledge mapping tools, including Citespace, Science of Science, VOSviewer, GPSvisualizer and Gephi software...
December 8, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27928710/synthesis-characterization-and-bioactivity-studies-of-novel-1-3-4-oxadiazole-small-molecule-that-targets-basic-phospholipase-a2-from-vipera-russelli
#9
Vivek Hamse Kameshwar, Kumar J R, Babu S Priya, S Nanjunda Swamy
Secretory phospholipase A2 (sPLA2) is a key enzyme participating in the inflammatory cascade followed by the action of cyclooxygenase-2 and lipoxygenases. Therefore, inhibitors of sPLA2 could be used as potent anti-inflammatory agents to treat the early phase of inflammation. In this study, we have prepared the fenoprofen and ibuprofen analogs containing 1,3,4-oxadiazole nucleus and tested against Vipera russelli venom's basic sPLA2 (VRV-PL-VIIIa). Among the tested ligands 5(a-t),2-(2-chlorophenyl)-5-(1-(4-phenoxyphenyl) ethyl)-1,3,4-oxadiazole (5m) inhibited the catalytic activity of VRV-PL-VIIIa with an IC50 value of 11...
December 7, 2016: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/27928588/investigation-of-the-binding-mode-of-1-3-4-oxadiazole-derivatives-as-amide-based-inhibitors-for-soluble-epoxide-hydrolase-seh-by-molecular-docking-and-mm-gbsa
#10
Leila Karami, Ali Akbar Saboury, Elham Rezaee, Sayyed Abbas Tabatabai
The soluble epoxide hydrolase (sEH) enzyme plays an important role in the metabolism of endogenous chemical mediators involved in the regulation of blood pressure and inflammation. Inhibition of sEH provides a new approach to the treatment of inflammation, hypertension and atherosclerosis. In this study, the binding modes and inhibition mechanisms of the new oxadiazole-based amide inhibitors of the human soluble epoxide hydrolase were investigated by molecular docking and molecular dynamics (MD) simulation followed by the MM-GBSA method to calculate the binding free energy of each inhibitor to sEH...
December 7, 2016: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27928570/photochemical-and-computational-studies-of-inclusion-complexes-between-%C3%AE-cyclodextrin-and-1-2-dihydroxyanthraquinones
#11
Sonaimuthu Mohandoss, Thambusamy Stalin
The formation of an inclusion complex between 1,2-dihydroxyanthraquinones (1,2-DHAQ) and β-cyclodextrin (β-CD) has been studied by UV-visible, fluorescence spectroscopy and electrochemical methods. The stoichiometric ratio of the inclusion complex was found to be 1 : 1 and the binding constant was evaluated using the Benesi-Hildebrand equation. The peak currents (Ipa and Ipc) change drastically with increasing β-CD concentration and the peak potentials (Epa and Epc) shifted. A mechanism is proposed to explain the inclusion process...
December 8, 2016: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/27927061/isolation-characterization-and-in-silico-in-vitro-and-in-vivo-antiulcer-studies-of-isoimperatorin-crystallized-from-ostericum-koreanum
#12
Hussain Raza, Qamar Abbas, Mubashir Hassan, Seong-Hui Eo, Zaman Ashraf, Daeyoung Kim, Abdul Rehman Phull, Song Ja Kim, Sung Kwon Kang, Sung-Yum Seo
CONTEXT: Ostericum koreanum (Maxim.) Kitagawa (Apiaceae) roots are traditionally used as an analgesic and antiulcer agent. However, the antiulcer potential of isoimperatorin isolated from O. koreanum has not yet been explored. AIM: To evaluate the antiulcer activity of isoimperatorin isolated from the roots of O. koreanum. MATERIALS AND METHODS: Isoimperatorin was isolated as cubic crystals by repeated column chromatography of the ethyl acetate fraction and structure was verified with (1)H NMR, (13)C NMR and high-resolution mass spectrometry (HRMS-FAB)...
December 2017: Pharmaceutical Biology
https://www.readbyqxmd.com/read/27926843/membrane-anchoring-and-ion-entry-dynamics-in-p-type-atpase-copper-transport
#13
Christina Grønberg, Oleg Sitsel, Erik Lindahl, Pontus Gourdon, Magnus Andersson
Cu(+)-specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu(+)-binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu(+) entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu(+) delivery...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27924680/atomic-insight-into-designed-carbamate-based-derivatives-as-acetylcholine-esterase-ache-inhibitors-a-computational-study-by-multiple-molecular-docking-and-molecular-dynamics-simulation
#14
Tecush Mohammadi, Yousef Ghayeb
Over 100 variants have been designed and studied, using multiple docking methods such as Autodock Vina, ArgusLab, Molegro Virtual Docker (MVD), and Hex-Cuda, to study the effect of alteration in the structure of carbamate based acetylcholyne esterase (AChE) inhibitors. 16 selected systems were then subjected to 14 ns molecular dynamics (MD) simulations. Results from all the docking methods are in agreement. Variants that involved biphenyl substituents possess the most negative binding energies in the -37.64 to -39...
December 7, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27924580/using-crispr-cas9-to-study-erk-signaling-in-drosophila
#15
Marta Forés, Aikaterini Papagianni, Laura Rodríguez-Muñoz, Gerardo Jiménez
Genome engineering using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated nuclease 9 (Cas9) technology is revolutionizing biomedical research. CRISPR-Cas9 enables precise editing of genes in a wide variety of cells and organisms, thereby accelerating molecular studies via targeted mutagenesis, epitope tagging, and other custom genetic modifications. Here, we illustrate the CRISPR-Cas9 methodology by focusing on Capicua (Cic), a nuclear transcriptional repressor directly phosphorylated and inactivated by ERK/MAPK...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924488/elucidating-mechanisms-of-molecular-recognition-between-human-argonaute-and-mirna-using-computational-approaches
#16
Hanlun Jiang, Lizhe Zhu, Amélie Héliou, Xin Gao, Julie Bernauer, Xuhui Huang
MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924486/surface-plasmon-resonance-a-useful-strategy-for-the-identification-of-small-molecule-argonaute-2-protein-binders
#17
Elena Poser, Ilaria Genovese, Silvia Masciarelli, Teresa Bellissimo, Francesco Fazi, Gianni Colotti
Surface plasmon resonance (SPR) is one of the most important techniques for the detection and the characterization of molecular interactions. SPR technology is a label-free approach for monitoring biomolecular interactions in real time. The binding of analytes to molecules immobilized on a thin metal film (ligand) determines a change in the refractive index and, therefore in the angle of extinction of light, is reflected when polarized light hits the film, monitored in real time as a change in the position of the dip in reflected intensity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924438/correlation-between-molecular-modelling-and-spectroscopic-techniques-in-investigation-with-dna-binding-interaction-of-ruthenium-ii-complexes
#18
REVIEW
B Thulasiram, C Shobha Devi, Yata Praveen Kumar, Rajeshwar Rao Aerva, S Satyanarayana, Penumaka Nagababu
The DNA binding studies of rutheniumu(II) polypyridyl complexes {[Ru(phen)2Mipc](2+), [Ru(bpy)2Mipc](2+), [Ru(dmb)2Mipc](2+), [Ru(phen)2BrIPC](2+), [Ru(bpy)2BrIPC](2+), [Ru(dmb)2BrIPC](2+), [Ru(phen)2PIP-Cl](2+), [Ru(bpy)2PIP-Cl](2+), [Ru(dmb)2PIP-Cl](2+), [Ru(phen)2IPPBA](2+), [Ru(bpy)2IPPBA](2+), [Ru(dmb)2IPPBA](2+)} with DNA investigated by electronic absorption titration, emission and molecular modelling studies to identify the binding interactions. All these complexes are showing good binding constant values ~10(4) to 10(5)...
December 6, 2016: Journal of Fluorescence
https://www.readbyqxmd.com/read/27924273/molecular-dynamics-analysis-to-evaluate-docking-pose-prediction
#19
Takako Sakano, Md Iqbal Mahamood, Takefumi Yamashita, Hideaki Fujitani
The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicted using a docking program. If the predicted pose is not unstable in an aqueous environment, MD simulation equilibrates the system and removes the ligand from the predicted position...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924272/in-silico-studies-for-the-interaction-of-tumor-necrosis-factor-alpha-tnf-%C3%AE-with-different-saponins-from-vietnamese-ginseng-panax-vietnamesis
#20
Oanh T P Kim, Manh D Le, Hoang X Trinh, Hai V Nong
Tumor necrosis factor-alpha (TNF-α) is a cytokine that plays an important role in inflammatory process and tumor development. Recent studies demonstrate that triterpene saponins from Vietnamese ginseng are efficient inhibitors of TNF-α. But the interactions between TNF-α and the saponins are still unclear. In this study, molecular docking and molecular dynamics simulations of TNF-α with three different triterpene saponins (majonoside R2, vina-ginsenoside R1 and vina-ginsenoside R2) were performed to evaluate their binding ability...
2016: Biophysics and Physicobiology
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