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https://www.readbyqxmd.com/read/28346800/using-chemoinformatics-bioinformatics-and-bioassay-to-predict-and-explain-the-antibacterial-activity-of-nonantibiotic-food-and-drug-administration-drugs
#1
Nour Aldin Kahlous, Muhammad Al Mohdi Bawarish, Muhammad Arabi Sarhan, Manfred Küpper, Ali Hasaba, Mazen Rajab
Discovering of new and effective antibiotics is a major issue facing scientists today. Luckily, the development of computer science offers new methods to overcome this issue. In this study, a set of computer software was used to predict the antibacterial activity of nonantibiotic Food and Drug Administration (FDA)-approved drugs, and to explain their action by possible binding to well-known bacterial protein targets, along with testing their antibacterial activity against Gram-positive and Gram-negative bacteria...
March 27, 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28345598/novel-1-4-dihydropyridines-for-l-type-calcium-channel-as-antagonists-for-cadmium-toxicity
#2
Madhu Sudhana Saddala, Ramesh Kandimalla, Pradeepkiran Jangampalli Adi, Sainath Sri Bhashyam, Usha Rani Asupatri
The present study, we design and synthesize the novel dihydropyridine derivatives, i.e., 3 (a-e) and 5 (a-e) and evaluated, anticonvulsant activity. Initially due to the lacuna of LCC, we modeled the protein through modeller 9.15v and evaluated through servers. Docking studies were performed with the synthesized compounds and resulted two best compounds, i.e., 5a, 5e showed the best binding energies. The activity of intracellular Ca(2+) measurements was performed on two cell lines: A7r5 (rat aortic smooth muscle cells) and SH-SY5Y (human neuroblastoma cells)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345459/n6-isopentenyladenosine-promoted-hela-cell-apoptosis-through-inhibitions-of-akt-and-transforming-growth-factor-%C3%AE-activated-kinase-1-activation
#3
Miao Li, Yonghao Qi, Jing Wei, Lulu Lu, Xuan Zhao, Lijun Zhou
N6-Isopentenyladenosine, a member of the family of plant hormones, possesses anti-cancer activities on a number of cancer cell lines. However, its mode of action in cervical cancer cell remains poorly understood. Our computational docking studies showed that N6-Isopentenyladenosine could bind with the really interesting new gene domain of tumor necrosis factor receptor-associated factor 6, which is an ubiquitination E3 ligase. Tumor necrosis factor receptor-associated factor 6-mediated ubiquitination is known to activate both protein kinase B (also known as AKT) and transforming growth factor β-activated kinase 1, and the really interesting new gene domain comprises the core of the ubiquitin ligase catalytic domain...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28345378/probing-the-behavior-of-bovine-serum-albumin-upon-binding-to-atenolol-insights-from-spectroscopic-and-molecular-docking-approaches
#4
Tuo-Ying Jiang, Kai-Li Zhou, Yan-Yue Lou, Dong-Qi Pan, Jie-Hua Shi
Molecular interaction of atenolol, a selective β1 receptor antagonist with the major carrier protein, bovine serum albumin (BSA), was investigated under imitated physiological conditions (pH 7.4) by means of fluorescence spectroscopy, UV absorption spectroscopy, Fourier transform infrared spectroscopy (FT-IR), and molecular modeling studies. The steady-state fluorescence spectra manifested that static type, due to formation of the atenolol-BSA complex, was the dominant mechanism for fluorescence quenching...
March 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28342427/spectroscopic-studies-of-the-interaction-mechanisms-between-mono-caffeoylquinic-acids-and-transferrin
#5
Yanqing Guan, Jing Dong, Shizhong Chen, Meixian Liu, Daidong Wang, Xiaotian Zhang, Hong Wang, Zongtao Lin
Transferrin (Tf) is an important protein responsible for circulating and transporting iron into cytoplasm. Tf can be taken into cells through endocytosis mediated by Tf receptor, which usually overexpresses in cancer cells. The Tf-Tf receptor pathway opens a possible avenue for novel targeted cancer therapy by utilizing Tf-binding active compounds. Among which, anti-cancer active caffeoylquinic acids (CQAs) were recently found to be promising Tf-binders by our group. For better understanding the anti-cancer activities of CQAs, it is important to unveil the binding mechanisms between CQAs and Tf...
March 7, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28342242/a-systematic-analysis-of-scoring-functions-in-rigid-body-protein-docking-the-delicate-balance-between-the-predictive-rate-improvement-and-the-risk-of-overtraining
#6
Didier Barradas-Bautista, Iain H Moal, Juan Fernández-Recio
Protein-protein interactions play fundamental roles in biological processes including signaling, metabolism and trafficking. While the structure of a protein complex reveals crucial details about the interaction, it is often difficult to acquire this information experimentally. As the number of interactions discovered increases faster than they can be characterized, protein-protein docking calculations may be able to reduce this disparity by providing models of the interacting proteins. Rigid-body docking is a widely used docking approach, and is often capable of generating a pool of models within which a near-native structure can be found...
March 25, 2017: Proteins
https://www.readbyqxmd.com/read/28341996/structural-insights-into-ligand-binding-of-pgrp1-splice-variants-in-chinese-giant-salamander-andrias-davidianus-from-molecular-dynamics-and-free-energy-calculations
#7
Zhitao Qi, Fancui Meng, Qihuan Zhang, Zisheng Wang, Guo Qiao, Wei Xu, Rong Shao, Chenglung Chen
Peptidoglycan (PGN) recognition proteins (PGRPs) are important pattern recognition receptors of the innate immune system. A number of PGRP splicing variants produced by alternative splicing of PGRP genes have been reported. However, several important aspects of interactions between PGRP splice variants and their ligands are still unclear. In the present study, three dimensional models of salamander PGRP1 (adPGRP1) and its splice variant (adPGRP1a) were constructed, and their key amino acids involved in interacting with PGNs were analyzed...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28341448/the-drosophila-dock-family-protein-sponge-is-required-for-development-of-the-air-sac-primordium
#8
Kazushge Morishita, Dang Ngoc Anh Suong, Hideki Yoshida, Masamitsu Yamaguchi
Dedicator of cytokinesis (DOCK) family genes are known as DOCK1-DOCK11 in mammals. DOCK family proteins mainly regulate actin filament polymerization and/or depolymerization and are GEF proteins, which contribute to cellular signaling events by activating small G proteins. Sponge (Spg) is a Drosophila counterpart to mammalian DOCK3/DOCK4, and plays a role in embryonic central nervous system development, R7 photoreceptor cell differentiation, and adult thorax development. In order to conduct further functional analyses on Spg in vivo, we examined its localization in third instar larval wing imaginal discs...
March 21, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28341137/targeting-hepatocellular-carcinoma-with-piperine-by-radical-mediated-mitochondrial-pathway-of-apoptosis-an-in-vitro-and-in-vivo-study
#9
Gunasekaran Vetrichelvi, Kannan Elangovan, S Niranjali Devaraj
Redox mediated cancer therapeutics are of immense interest in the recent decade due to their anticancer activity. Piperine is the principal alkaloid of black and long pepper. Although its anticancer activity has been reported in number of cancers , the precise molecular mechanism of action remains to be unravelled. Hence, in this study, for the first time, we delineated the mechanistic insight into the effect of piperine against hepatocellular carcinoma (HCC).MTT analysis determined the dose and time dependent cytotoxicity of piperine against Hep G2 cells...
March 21, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28340988/rational-design-synthesis-and-structure-activity-relationships-of-5-amino-1h-pyrazole-4-carboxylic-acid-derivatives-as-protein-tyrosine-phosphatase-1b-inhibitors
#10
Sujay Basu, Philip Prathipati, Sachin Thorat, Shariq Ansari, Meena Patel, Vaibhav Jain, Ramana R Jinugu, Sanjay Niranjan, Siddhartha De, Satyanarayana Reddy
A series of novel amino-carboxylic based pyrazole as protein tyrosine phosphatase 1B (PTP1B) inhibitors were designed on the basis of structure-based pharmacophore model and molecular docking. Compounds containing different hydrophobic tail (1,2-diphenyl ethanone, oxdiadizole and dibenzyl amines) were synthesized and evaluated in PTP1B enzymatic assay. Structure-activity relationship based optimization resulted in identification of several potent, metabolically stable and cell permeable PTP1B inhibitors.
January 1, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28340400/pharmacoinformatics-exploration-of-polyphenol-oxidases-leading-to-novel-inhibitors-by-virtual-screening-and-molecular-dynamic-simulation-study
#11
Mubashir Hassan, Qamar Abbas, Zaman Ashraf, Ahmed A Moustafa, Sung-Yum Seo
Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis...
March 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28339004/cyclocurcumin-a-curcumin-derivative-exhibits-immune-modulating-ability-and-is-a-potential-compound-for-the-treatment-of-rheumatoid-arthritis-as-predicted-by-the-mm-pbsa-method
#12
Min Fu, Lihui Chen, Limin Zhang, Xiao Yu, Qingrui Yang
The control and treatment of rheumatoid arthritis is a challenge in today's world. Therefore, the pursuit of natural disease-modifying antirheumatic drugs (DMRDs) remains a top priority in rheumatology. The present study focused on curcumin and its derivatives in the search for new DMRDs. We focused on prominent p38 mitogen-activated protein (MAP) kinase p38α which is a prime regulator of tumor necrosis factor-α (TNF-α), a key mediator of rheumatoid arthritis. In the present study, we used the X-ray crystallographic structure of p38α for molecular docking simulations and molecular dynamic simulations to study the binding modes of curcumin and its derivatives with the active site of p38α...
March 20, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28338692/computational-design-of-self-assembling-cyclic-protein-homo-oligomers
#13
Jorge A Fallas, George Ueda, William Sheffler, Vanessa Nguyen, Dan E McNamara, Banumathi Sankaran, Jose Henrique Pereira, Fabio Parmeggiani, T J Brunette, Duilio Cascio, Todd R Yeates, Peter Zwart, David Baker
Self-assembling cyclic protein homo-oligomers play important roles in biology, and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue-pair-transform method to assess the designability of a protein-protein interface. This method is sufficiently rapid to enable the systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28338290/identification-of-natural-inhibitors-of-bcr-abl-for-the-treatment-of-chronic-myeloid-leukemia
#14
Phani Krishna, Sailu Sarvagalla, Bindu Madhuri, Sankar Pajaniradje, Vinitha Baskaran, Mohane Selvaraj Coumar, R Baskaran
Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder of the hematopoietic stem cells, characterized at the molecular level by the bcr/abl gene rearrangement. Even though targeting the fusion gene product Bcr-Abl protein is a successful strategy, development of drug resistance and drug intolerance are currently the limitations for Bcr-Abl targeted CML therapy. With an aim to develop natural Bcr-Abl inhibitors, we performed virtual screening (VS) of ZINC natural compound database by docking with Abl kinase using Glide software...
March 24, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28337317/structural-requirements-of-hdac-inhibitors-saha-analogues-modified-at-the-c2-position-display-hdac6-8-selectivity
#15
Ahmed T Negmeldin, Geetha Padige, Anton V Bieliauskas, Mary Kay H Pflum
Histone deacetylase (HDAC) proteins are epigenetic regulators that deacetylate protein substrates, leading to subsequent changes in cell function. HDAC proteins are implicated in cancers, and several HDAC inhibitors have been approved by the FDA as anticancer drugs, including SAHA (suberoylanilide hydroxamic acid; Vorinostat and Zolinza). Unfortunately, SAHA inhibits most HDAC isoforms, which limits its use as a pharmacological tool and may lead to side effects in the clinic. In this work SAHA analogues substituted at the C2 position were synthesized and screened for HDAC isoform selectivity in vitro and in cells...
March 9, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28336274/characterization-molecular-docking-dynamics-simulation-and-metadynamics-of-kisspeptin-receptor-with-kisspeptin
#16
Mohd Ashraf Rather, Syed Hussain Basha, Irfan Ahmad Bhat, Niti Sharma, Priyanka Nandanpawar, Mohan Badhe, Gireesh-Babu P, Aparna Chaudhari, Jitendra Kumar Sundaray, Rupam Sharma
We report molecular characterization of the kisspeptin receptor (kiss1r), an essential gatekeeper for reproduction and onset of puberty in vertebrates. The full-length cDNA sequence of kiss1r is 1786bp which consist of 5' UTR (untranslated region) 261bp, 3' UTR of 424bp and open reading frame of 1101 encoding a putative protein of 366 amino acids. Basal tissue expression pattern of kiss1r mRNA revealed that it is mainly expressed in the brain and testis. We also report the structure of the kiss1r, along with plausible activation mechanism of this receptor by kisspeptin using computational modelling and dynamic simulation approach of multiple 100ns of timescale...
March 20, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28335409/the-formyl-peptide-receptors-diversity-of-ligands-and-mechanism-for-recognition
#17
REVIEW
Hui-Qiong He, Richard D Ye
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors...
March 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28334282/comprehensive-assessment-of-flexible-ligand-docking-algorithms-current-effectiveness-and-challenges
#18
Sheng-You Huang
Protein-ligand docking has been playing an important role in modern drug discovery. To model drug-target binding in real systems, a number of flexible-ligand docking algorithms with different sampling strategies and scoring methods have been subsequently developed over the past three decades, while rigid-ligand docking is still being used because of its compelling computational efficiency. Here, a comprehensive assessment has been conducted to investigate the effectiveness of flexible-ligand docking versus rigid-ligand docking for three representative docking algorithms (global optimization, incremental construction and multi-conformer docking) in virtual screening and pose prediction on the Directory of Useful Decoys...
March 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334258/review-and-comparative-assessment-of-sequence-based-predictors-of-protein-binding-residues
#19
Jian Zhang, Lukasz Kurgan
Understanding of molecular mechanisms that govern protein-protein interactions and accurate modeling of protein-protein docking rely on accurate identification and prediction of protein-binding partners and protein-binding residues. We review over 40 methods that predict protein-protein interactions from protein sequences including methods that predict interacting protein pairs, protein-binding residues for a pair of interacting sequences and protein-binding residues in a single protein chain. We focus on the latter methods that provide residue-level annotations and that can be broadly applied to all protein sequences...
March 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28330605/polyubiquitin-photoactivatable-crosslinking-reagents-for-mapping-ubiquitin-interactome-identify-rpn1-as-a-proteasome-ubiquitin-associating-subunit
#20
Michal Chojnacki, Wissam Mansour, Dharjath S Hameed, Rajesh K Singh, Farid El Oualid, Rina Rosenzweig, Mark A Nakasone, Zanlin Yu, Fabian Glaser, Lewis E Kay, David Fushman, Huib Ovaa, Michael H Glickman
Ubiquitin (Ub) signaling is a diverse group of processes controlled by covalent attachment of small protein Ub and polyUb chains to a range of cellular protein targets. The best documented Ub signaling pathway is the one that delivers polyUb proteins to the 26S proteasome for degradation. However, studies of molecular interactions involved in this process have been hampered by the transient and hydrophobic nature of these interactions and the lack of tools to study them. Here, we develop Ub-phototrap (Ub(PT)), a synthetic Ub variant containing a photoactivatable crosslinking side chain...
March 16, 2017: Cell Chemical Biology
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