keyword
MENU ▼
Read by QxMD icon Read
search

protein docking

keyword
https://www.readbyqxmd.com/read/28636189/discovery-of-alkyl-bis-oxy-dibenzimidamide-derivatives-as-novel-protein-arginine-methyltransferase-1-prmt1-inhibitors
#1
Wei-Yao Zhang, Wen-Chao Lu, Hao Jiang, Zheng-Bing Lv, Yi-Qian Xie, Fu-Lin Lian, Zhong-Jie Liang, Yu-Xi Jiang, Da-Jin Wang, Cheng Luo, Jia Jin, Fei Ye
Protein arginine methylation, a post-translational modification critical for a variety of biological processes, is catalyzed by protein arginine N-methyltransferases (PRMTs). In particular, PRMT1 is responsible for over 85% of the arginine methylation in mammalian cells. Dysregulation of PRMT1 is involved in diverse pathological diseases including cancers. However, most current PRMT1inhibitors are lack of specificity, efficacy, and bioavailability. Herein, a series of alkyl bis(oxy)dibenzimidamide derivatives were identified as selective PRMT1 inhibitors...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28634712/site-directed-mutagenesis-under-the-direction-of-in-silico-protein-docking-modeling-reveals-the-active-site-residues-of-3-ketosteroid-%C3%AE-1-dehydrogenase-from-mycobacterium-neoaurum
#2
Ning Qin, Yanbing Shen, Xu Yang, Liqiu Su, Rui Tang, Wei Li, Min Wang
3-Ketosteroid-Δ(1)-dehydrogenases (KsdD) from Mycobacterium neoaurum could transform androst-4-ene-3,17-dione (AD) to androst-1,4-diene-3,17-dione. This reaction has a significant effect on the product of pharmaceutical steroid. The crystal structure and active site residues information of KsdD from Mycobacterium is not yet available, which result in the engineering of KsdD is tedious. In this study, by the way of protein modeling and site-directed mutagenesis, we find that, Y122, Y125, S138, E140 and Y541 from the FAD-binding domain and Y365 from the catalytic domain play a key role in this transformation...
July 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28634376/structural-basis-to-stabilize-the-domain-motion-of-bard1-ard-brct-by-cstf50
#3
Rajan Kumar Choudhary, Mohd Quadir Siddiqui, Pankaj S Thapa, Nikhil Gadewal, Senthil Kumar Nachimuthu, Ashok K Varma
BRCA1 associated ring domain protein 1(BARD1) is a tumor suppressor protein having a wide role in cellular processes like cell-cycle checkpoint, DNA damage repair and maintenance of genomic integrity. Germ-line mutation Gln 564 His discovered in linker region of BARD1 leads to loss of binding to Cleavage stimulating factor (CstF50), which in turn instigates the premature mRNA transcript formation and apoptosis. We have studied the dynamics of ARD domain present in the BARD1 wild-type and mutant protein in association with CstF50 using biophysical, biochemical and molecular dynamics simulations...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634119/an-ultrasensitive-stain-for-negative-protein-detection-in-sds-page-via-4-5-dibromofluorescein
#4
Dongdong Yu, Yang Wang, Shaoqing Zhang, Zhiwei Chen, Mei Xue, Ying Wang, Weitao Cong, Litai Jin, Zhongxin Zhu
A highly sensitive method for brief and economical staining of proteins in 1-D and 2-D sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) by 4',5'-Dibromofluorescein (DBF) was developed in this study. Down to 0.025-0.05ng protein could be detected within 10min (only 2 steps) by DBF stain, which is approximately 10-fold more sensitive than those of Eosin Y (EY) and SYPRO Ruby stains, and 20-fold more sensitive than that of imidazole-zinc (IZ) negative stain. In addition, the LC-MS/MS results indicated that the newly developed staining method is compatible with the downstream protein identification...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28633568/the-potential-inhibitory-effect-of-%C3%AE-casein-on-the-aggregation-and-deposition-of-a%C3%AE-1-42-fibrils-in-alzheimer-s-disease-insight-from-in-vitro-and-in-silico-studies
#5
Sedighehsadat Hojati, Arezou Ghahghaei, Milad Lagzian
Aβ1-40 and Aβ1-42 have been shown to be the main components of the amyloid plaques found in the extracellular environment of neurons in Alzheimer's disease. β-Casein, a milk protein, has been shown to display a remarkable chaperone ability in preventing the aggregation of proteins. In this study, the ability of β-casein to suppress the amyloid fibril formation of Aβ1-42 has been examined through in vitro studies and molecular docking simulation. The results demonstrate the inhibitory effect of β-casein on fibril formation in Aβ1-42, in a concentration dependent manner, suggesting that the chaperone binds to the Aβ1-42 and prevents amyloid fibril formation...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28633528/the-binding-space-concept-a-new-approach-to-enhance-the-reliability-of-docking-scores-and-its-application-to-predicting-butyrylcholinesterase-bche-hydrolytic-activity
#6
Giulio Vistoli, Angelica Mazzolari, Bernard Testa, Alessandro Pedretti
Docking simulations are very popular approaches able to assess the capacity of a given ligand to interact with a target. Docking simulations are usually focused on a single best complex even though many studies showed that ligands retain a significant mobility within a binding pocket by assuming different binding modes all of which may contribute to the monitored ligand affinity. The present study describes an innovative concept, the binding space, which allows an exploration of the ligand mobility within the binding pocket by simultaneously considering several ligand poses as generated by docking simulations...
June 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28633380/epigallocatechin-3-gallate-and-related-phenol-compounds-redirect-the-amyloidogenic-aggregation-pathway-of-ataxin-3-towards-non-toxic-aggregates-and-prevent-toxicity-in-neural-cells-and-caenorhabditis-elegans-animal-model
#7
Cristina Visentin, Francesca Pellistri, Antonino Natalello, Jacopo Vertemara, Marcella Bonanomi, Elena Gatta, Amanda Penco, Annalisa Relini, Luca De Gioia, Cristina Airoldi, Maria E Regonesi, Paolo Tortora
The protein ataxin-3 (ATX3) triggers an amyloid-related neurodegenerative disease when its polyglutamine stretch is expanded beyond a critical threshold. We formerly demonstrated that the polyphenol epigallocatechin-3-gallate (EGCG) could redirect amyloid aggregation of a full-length, expanded ATX3 (ATX3-Q55) towards non-toxic, soluble, SDS-resistant aggregates. Here, we have characterized other related phenol compounds, although smaller in size, i.e., (-)-epigallocatechin gallate (EGC), and gallic acid (GA)...
June 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28632334/functional-analysis-of-female-biased-odorant-binding-protein-6-for-volatile-and-nonvolatile-host-compounds-in-adelphocoris-lineolatus-goeze
#8
L Sun, Q Wang, S Yang, Q Wang, Z Zhang, A Khashaveh, Y-J Zhang, Y-Y Guo
The polyphagous mirid bug Adelphocoris lineolatus relies heavily on olfactory cues to track suitable host plants. Thus, a better understanding of the molecular basis of its olfactory detection could contribute to the development of effective pest management strategies. In the present study, we report the expression profile of the odorant binding protein gene A. lineolatus odorant binding protein 6 (AlinOBP6). Quantitative real-time PCR experiments suggest that AlinOBP6 is female adult antennae-biased. Cellular immunolocalization analyses show that AlinOBP6 is highly expressed in the lymph of both multiporous sensilla basiconica and uniporous sensilla chaetica...
June 20, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28630008/contribution-of-the-carbohydrate-binding-ability-of-vatairea-guianensis-lectin-to-induce-edematogenic-activity
#9
Gabriela F O Marques, Vinicius J S Osterne, Livia M Almeida, Luiz A C Brizeno, Vanir R Pinto-Junior, Mayara Q Santiago, Antonio H B Neco, Mario R L Mota, Luiz A G Souza, Kyria S Nascimento, Alana F Pires, Benildo S Cavada, Ana M S Assreuy
Vatairea guianensis lectin (VGL), Dalbergiae tribe, is a N-acetyl-galactosamine (GalNAc)/Galactose (Gal) lectin previously purified and characterized. In this work, we report its structural features, obtained from bioinformatics tools, and its inflammatory effect, obtained from a rat paw edema model. The VGL model was obtained by homology with the lectin of Vatairea macrocarpa (VML) as template, and we used it to demonstrate the common characteristics of legume lectins, such as the jellyroll motif and presence of a metal-binding site in the vicinity of the carbohydrate-recognition domain (CRD)...
June 16, 2017: Biochimie
https://www.readbyqxmd.com/read/28629184/determination-of-structural-requirements-of-n-substituted-tetrahydro-%C3%AE-carboline-imidazolium-salt-derivatives-using-in-silico-approaches-for-designing-mek-1-inhibitors
#10
Jingwei Liang, Mingyang Wang, Xinyang Li, Xin He, Chong Cao, Fanhao Meng
Novel N-substituted tetrahydro-β-carboline imidazolium salt derivatives proved to have potent antitumor activity in past research. The Topomer CoMFA and CoMSIA function in Sybyl-X 2.0 software was applied for the identification of important features of N-substituted tetrahydro-β-carboline-imidazolium salt derivative moieties. In the case of Topomer CoMFA, all the compounds were split into two fragments which were used to generate a 3D invariant representation, the statistical results of the Topomer CoMFA model: q² value of 0...
June 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28629119/cholinesterase-inhibitory-activities-of-adamantyl-based-derivatives-and-their-molecular-docking-studies
#11
Huey Chong Kwong, Siau Hui Mah, Tze Shyang Chia, Ching Kheng Quah, Gin Keat Lim, C S Chidan Kumar
Adamantyl-based compounds are clinically important for the treatments of type 2 diabetes and for their antiviral abilities, while many more are under development for other pharmaceutical uses. This study focused on the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitory activities of adamantyl-based ester derivatives with various substituents on the phenyl ring using Ellman's colorimetric method. Compound 2e with a 2,4-dichloro electron-withdrawing substituent on the phenyl ring exhibited the strongest inhibition effect against AChE, with an IC50 value of 77...
June 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28628858/unravelling-the-structural-interactions-between-pkr-kinase-domain-and-its-small-molecule-inhibitors-using-computational-approaches
#12
Sagar Barage, Abhijeet Kulkarni, Jayanta K Pal, Manali Joshi
The RNA-dependent protein kinase (PKR), an eIF2α kinase plays an important role in anti-viral response, apoptosis and cell survival. It is also implicated to play a role in several cancers, metabolic and neurodegenerative disorders. A few ATP competitive inhibitors of the PKR have been reported in the literature with promising results in vitro and in vivo. The aim of this study was to unravel the structural interactions between these inhibitors and the PKR kinase domain using molecular simulations and docking...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28627969/identification-of-potential-inhibitors-of-fasciola-gigantica-thioredoxin1-computational-screening-molecular-dynamics-simulation-and-binding-free-energy-studies
#13
Rohit Shukla, Harish Shukla, Parismita Kalita, Amit Sonkar, Tripti Pandey, Dev Bukhsh Singh, Awanish Kumar, Timir Tripathi
Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score...
June 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28626530/discovery-of-a-series-of-indazole-trpa1-antagonists
#14
David C Pryde, Brian E Marron, Christopher W West, Steven Reister, George Amato, Katrina Yoger, Brett Antonio, Karen Padilla, Peter J Cox, Jamie Turner, Joseph S Warmus, Nigel A Swain, Kiyoyuki Omoto, John H Mahoney, Aaron C Gerlach
A series of TRPA1 antagonists is described which has as its core structure an indazole moiety. The physical properties and in vitro DMPK profiles are discussed. Good in vivo exposure was obtained with several analogs, allowing efficacy to be assessed in rodent models of inflammatory pain. Two compounds showed significant activity in these models when administered either systemically or topically. Protein chimeras were constructed to indicate compounds from the series bound in the S5 region of the channel, and a computational docking model was used to propose a binding mode for example compounds...
June 8, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28626481/quantum-mechanical-molecular-mechanical-and-docking-study-of-the-novel-analogues-based-on-hybridization-of-common-pharmacophores-as-potential-anti-breast-cancer-agents
#15
Parvin Asadi, Ghadamali Khodarahmi, Hossein Farrokhpour, Farshid Hassanzadeh, Lotfollah Saghaei
In an attempt to identify some new potential leads as anti-breast cancer agents, novel hybrid compounds were designed by molecular hybridization approach. These derivatives were structurally derived from hybrid benzofuran-imidazole and quinazolinone derivatives, which had shown good cytotoxicity against the breast cancer cell line (MCF-7). Since aromatase enzyme (CYP19) is highly expressed in the MCF-7 cell line, the binding of these novel hybrid compounds to aromatase was investigated using the docking method...
June 2017: Research in Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28626477/in-vitro-evaluation-of-dihydropyridine-3-carbonitriles-as-potential-cytotoxic-agents-through-pim-1-protein-kinase-inhibition
#16
Khalil Abnous, Hesam Manavi, Soghra Mehri, Mona Alibolandi, Hossein Kamali, Morteza Ghandadi, Farzin Hadizadeh
PIM-1 protein kinase inhibitor belongs to a novel class of serine/threonine kinases. As PIM-1 is overexpressed in cancer cells and possesses oncogenic functions, its inhibition provides a new option in cancer therapy. In this study, in vitro inhibitory effects of seven analogues of 1, 2-dihydropyridine-3-carbonitrile derivatives Ia-c, IIa-d on the activity of recombinant PIM-1 were evaluated using dimethylthiazol diphenyltetrazolium bromide (MTT) assay. The PIM-1 protein kinase inhibitory potencies and the cytotoxicity effects of tested compounds were respectively as follows: Ic > IIa > Ia > IIb > Ib > IId > IIc and IIb > IIa > Ia > IIc > Ic > Ib > IId, respectively...
June 2017: Research in Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28625885/dock8-deficiency-insights-into-pathophysiology-clinical-features-and-management
#17
REVIEW
Catherine M Biggs, Sevgi Keles, Talal A Chatila
Dedicator of Cytokinesis 8 (DOCK8) deficiency is a combined immunodeficiency that exemplifies the broad clinical features of primary immunodeficiencies (PIDs), extending beyond recurrent infections to include atopy, autoimmunity and cancer. It is caused by loss of function mutations in DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes that regulates the actin cytoskeleton. Additional roles of DOCK8 have also emerged, including regulating MyD88-dependent Toll-like receptor signaling and the activation of the transcription factor STAT3...
June 15, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28625790/preprotein-conformational-dynamics-drive-bivalent-translocase-docking-and-secretion
#18
Marios Frantzeskos Sardis, Alexandra Tsirigotaki, Katerina Elias Chatzi, Athina George Portaliou, Giorgos Gouridis, Spyridoula Karamanou, Anastassios Economou
Most bacterial secretory proteins destined beyond the plasma membrane are secreted post-translationally by the Sec translocase. In the first step of translocation, preproteins are targeted for binding to their 2-site receptor SecA, the peripheral ATPase subunit of the translocase. We now reveal that secretory preproteins use a dual-key mechanism to bridge the signal peptide and mature domain receptor sites and cooperatively enhance their affinities. Docking of targeting-competent mature domains requires that their extensive disorder is finely tuned...
June 5, 2017: Structure
https://www.readbyqxmd.com/read/28625779/multiple-isoforms-of-nesprin1-are-integral-components-of-ciliary-rootlets
#19
Chloe Potter, Wanqiu Zhu, David Razafsky, Philip Ruzycki, Alexander V Kolesnikov, Teresa Doggett, Vladimir J Kefalov, Ewelina Betleja, Moe R Mahjoub, Didier Hodzic
SYNE1 (synaptic nuclear envelope 1) encodes multiple isoforms of Nesprin1 (nuclear envelope spectrin 1) that associate with the nuclear envelope (NE) through a C-terminal KASH (Klarsicht/Anc1/Syne homology) domain (Figure 1A) [1-4]. This domain interacts directly with the SUN (Sad1/Unc84) domain of Sun proteins [5-7], a family of transmembrane proteins of the inner nuclear membrane (INM) [8, 9], to form the so-called LINC complexes (linkers of the nucleoskeleton and cytoskeleton) that span the entire NE and mediate nuclear positioning [10-12]...
June 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28625565/the-cep19-rabl2-gtpase-complex-binds-ift-b-to-initiate-intraflagellar-transport-at-the-ciliary-base
#20
Tomoharu Kanie, Keene Louis Abbott, Nancie Ann Mooney, Edward Douglas Plowey, Janos Demeter, Peter Kent Jackson
Highly conserved intraflagellar transport (IFT) protein complexes direct both the assembly of primary cilia and the trafficking of signaling molecules. IFT complexes initially accumulate at the base of the cilium and periodically enter the cilium, suggesting an as-yet-unidentified mechanism that triggers ciliary entry of IFT complexes. Using affinity-purification and mass spectrometry of interactors of the centrosomal and ciliopathy protein, CEP19, we identify CEP350, FOP, and the RABL2B GTPase as proteins organizing the first known mechanism directing ciliary entry of IFT complexes...
June 14, 2017: Developmental Cell
keyword
keyword
82202
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"