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https://www.readbyqxmd.com/read/28938109/investigating-mutation-specific-biological-activities-of-small-molecules-using-quantitative-structure-activity-relationship-for-epidermal-growth-factor-receptor-in-cancer
#1
P Anoosha, R Sakthivel, M Michael Gromiha
Epidermal Growth Factor Receptor (EGFR) is a potential drug target in cancer therapy. Missense mutations play major roles in influencing the protein function, leading to abnormal cell proliferation and tumorigenesis. A number of EGFR inhibitor molecules targeting ATP binding domain were developed for the past two decades. Unfortunately, they become inactive due to resistance caused by new mutations in patients, and previous studies have also reported noticeable differences in inhibitor binding to distinct known driver mutants as well...
August 26, 2017: Mutation Research
https://www.readbyqxmd.com/read/28938069/molecular-recognition-of-agonists-and-antagonists-by-the-nucleotide-activated-g-protein-coupled-p2y2-receptor
#2
Muhammad Rafehi, Alexander Neumann, Younis Baqi, Enas M Malik, Michael Wiese, Vigneshwaran Namasivayam, Christa E Müller
A homology model of the nucleotide-activated P2Y2R was created based on the X-ray structures of the P2Y1 and P2Y12 receptors. Docking studies were performed, and receptor mutants were created to probe the identified binding interactions. Mutation of residues predicted to interact with the ribose (Arg110) and the phosphates of the nucleotide agonists (Arg265, Arg292) or that contribute indirectly to binding (Tyr288) abolished activity. The Y114F, R194A, and F261A mutations led to inactivity of diadenosine tetraphosphate and to a reduced response of UTP...
September 22, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28937847/toxic-interaction-mechanism-of-two-fluoroquinolones-with-serum-albumin-by-spectroscopic-and-computational-methods
#3
Pengfei Qin, Xingren Pan, Rutao Liu, Changwei Hu, Yuliang Dong
To evaluate the toxicity of two fluoroquinolones (FQs), ciprofloxacin (CPFX), and enrofloxacin (ENFX), at the protein level, their binding modes with bovine serum albumin (BSA) were characterized by multiple spectroscopic and molecular docking methods under simulated physiological conditions. On the basis of fluorescence spectra, we concluded that both FQs greatly quenched the fluorescence intensity of BSA, which was attributed to the formation of a moderately strong complex mainly through electrostatic interactions...
September 22, 2017: Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes
https://www.readbyqxmd.com/read/28937618/novel-fxa-inhibitor-identification-through-integration-of-ligand-and-structure-based-approaches
#4
Carlos F Lagos, Gerardine F Segovia, Nicolás Nuñez-Navarro, Mario A Faúndez, Flavia C Zacconi
Factor Xa (FXa), a vitamin K-dependent serine protease plays a pivotal role in the coagulation cascade, one of the most interesting targets for the development of new anticoagulants. In the present work, we performed a virtual screening campaign based on ligand-based shape and electrostatic similarity search and protein-ligand docking to discover novel FXa-targeted scaffolds for further development of inhibitors. From an initial set of 260,000 compounds from the NCI Open database, 30 potential FXa inhibitors were identified and selected for in vitro biological evaluation...
September 22, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28935251/leachable-diphenylguanidine-from-rubber-closures-used-in-pre-filled-syringes-a-case-study-to-understand-solid-and-solution-interactions-with-oxytocin
#5
Ahmed S Zidan, Sabir M Aqueel, Alaadin Alayoubi, Adil Mohammad, Jinhui Zhang, Ziyaur Rahman, Patrick Faustino, Richard T Lostritto, Muhammad Ashraf
Leachables derived from multi-component drug-device syringe systems can result in changes to the quality of drug products. Diphenylguanidine (DPG), a leachable released from styrene butadiene rubber syringe plungers, interacts with Oxytocin to form protein-adducts. This study investigated the mechanism and kinetics of this interaction in both solid and solution states through in-vitro tests and spectroscopic methods For solid state interaction, the protein-adducts with DPG were characterized using SEM, XRD, DSC, FTIR, (13)C ss NMR, and dissolution analysis...
September 18, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28935134/sites-contributing-to-trpa1-activation-by-the-anesthetic-propofol-identified-by-photoaffinity-labeling
#6
Kellie A Woll, Kenneth A Skinner, Eleonora Gianti, Natarajan V Bhanu, Benjamin A Garcia, Vincenzo Carnevale, Roderic G Eckenhoff, Rachelle Gaudet
In addition to inducing anesthesia, propofol activates a key component of the pain pathway, the transient receptor potential ankyrin 1 ion channel (TRPA1). Recent mutagenesis studies suggested a potential activation site within the transmembrane domain, near the A-967079 cavity. However, mutagenesis cannot distinguish between protein-based and ligand-based mechanisms, nor can this site explain the complex modulation by propofol. Thus more direct approaches are required to reveal potentially druggable binding sites...
September 19, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28934646/clerodane-diterpenoids-from-scutellaria-formosana-with-inhibitory-effects-on-no-production-and-interactions-with-inos-protein
#7
Peixia Wang, Feng Liu, Xueyuan Yang, Yue Liang, Shen Li, Guochen Su, Da-Qing Jin, Yasushi Ohizumi, Jing Xu, Yuanqiang Guo
A phytochemical study on Scutellaria formosana afforded five previously undescribed spiro-diterpenoids, scutellapenes A-E. The structures were elucidated on the basis of extensive 1D and 2D NMR spectroscopic data analysis, and the absolute configurations of these compounds were established by the time-dependent density functional theory (TDDFT) electronic circular dichroism (ECD) calculations. Scutellapenes B-E possess a spiro-diterpenoid skeleton. All of the compounds showed inhibitory effects on LPS-induced nitric oxide (NO) production in murine microglial BV-2 cells...
September 18, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28934328/the-human-vgf-derived-bioactive-peptide-tlqp-21-binds-heat-shock-71-kda-protein-8-hspa8-on-the-surface-of-sh-sy5y-cells
#8
Shamim Akhter, Sandipan Chakraborty, Daniela Moutinho, Elia Álvarez-Coiradas, Isaac Rosa, Juan Viñuela, Eduardo Domínguez, Angel García, Jesús R Requena
VGF (non-acronymic)is a secreted chromogranin/secretogranin that gives rise to a number of bioactive peptides by a complex proteolysis mechanism. VGF-derived peptides exert an extensive array of biological effects in energy metabolism, mood regulation, pain, gastric secretion function, reproduction and, perhaps, cancer. It is therefore surprising that very little is known about receptors and binding partners of VGF-derived peptides and their downstream molecular mechanisms of action. Here, using affinity chromatography and mass spectrometry-based protein identification, we have identified the heat shock cognate 71 kDa protein A8 (HSPA8)as a binding partner of human TLQP-21 on the surface of human neuroblastomaSH-SY5Y cells...
2017: PloS One
https://www.readbyqxmd.com/read/28933851/design-and-structure-guided-development-of-novel-inhibitors-of-the-xeroderma-pigmentosum-group-a-xpa-protein-dna-interaction
#9
Navnath S Gavande, Pamela VanderVere-Carozza, Akaash K Mishra, Tyler L Vernon, Katherine S Pawelczak, John J Turchi
XPA is a unique and essential protein required for the nucleotide excision DNA repair pathway and represents a therapeutic target in oncology. Herein, we are the first to develop novel inhibitors of the XPA-DNA interaction through structure-guided drug design efforts. Ester derivatives of the compounds 1 (X80), 22, and 24 displayed excellent inhibitory activity (IC50 of 0.82 ± 0.18 μM and 1.3 ± 0.22 μM, respectively) but poor solubility. We have synthesized novel amide derivatives that retain potency and have much improved solubility...
September 21, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28933546/rational-design-of-selective-adenine-based-scaffolds-for-inactivation-of-bacterial-histidine-kinases
#10
Manibarsha Goswami, Kaelyn E Wilke, Erin E Carlson
Bacterial histidine kinases (HKs) are quintessential regulatory enzymes found ubiquitously in bacteria. Apart from regulatory roles, they are also involved in the production of virulence factors and conferring resistance to various antibiotics in pathogenic microbes. We have previously reported compounds that inhibit multiple HKs by targeting the conserved catalytic and ATP-binding (CA) domain. Herein, we conduct a detailed structure-activity relationship assessment of adenine-based inhibitors using biochemical and docking methods...
September 21, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28933241/characterization-of-human-s-adenosyl-homocysteine-hydrolase-in-vitro-and-identification-of-its-potential-inhibitors
#11
Weiwei Hao, Yanhua Li, Qiuli Shan, Tian Han, Wencheng Li, Sheng He, Kongkai Zhu, Yumei Li, Xiaojun Tan, Jinsong Gu
Human S-adenosyl-homocysteine hydrolase (SAHH, E.C.3.3.1.1) has been considered to be an attractive target for the design of medicines to treat human disease, because of its important role in regulating biological methylation reactions to catalyse the reversible hydrolysis of S-adenosylhomocysteine (SAH) to adenosine (Ado) and l-homocysteine (Hcy). In this study, SAHH protein was successfully cloned and purified with optimized, Pichia pastoris (P. pastoris) expression system. The biological activity results revealed that, among the tested compounds screened by ChemMapper and SciFinder Scholar, 4-(3-hydroxyprop-1-en-1-yl)-2-methoxyphenol (coniferyl alcohol, CAS: 458-35-5, ZINC: 12359045) exhibited the highest inhibition against rSAHH (IC50= 34 nM)...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28932739/agonist-binding-to-chemosensory-receptors-a-systematic-bioinformatics-analysis
#12
Fabrizio Fierro, Eda Suku, Mercedes Alfonso-Prieto, Alejandro Giorgetti, Sven Cichon, Paolo Carloni
Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28932107/bioinformatics-study-of-m-9053g-a-mutation-at-the-atp6-gene-in-relation-to-type-2-diabetes-mellitus-and-cataract-diseases
#13
Iman Permana Maksum, Sandy Risfi Saputra, Nenden Indrayati, Muhammad Yusuf, Toto Subroto
The mitochondrial disease often associated with various illnesses in relation to the activity of cells metabolites and the synthesis of adenosine triphosphate (ATP), including alteration in the mitochondrial DNA. The mutation of m.9053G>A at the ATP6 gene was found in patients with type 2 diabetes mellitus (DM type 2) and cataract. Therefore, this mutation is predicted to be clinical features of the 2 diseases. ATP6 gene encodes protein subunit of ATPase6, a part of ATP synthase, which is important in the electron transfer and proton translocation in intracellular respiration system...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28931425/neutralizing-immune-responses-induced-by-oligomeric-h5n1-hemagglutinins-from-plants
#14
Hoang Trong Phan, Thuong Thi Ho, Ha Hoang Chu, Trang Huyen Vu, Ulrike Gresch, Udo Conrad
Plant-based transient expression is an alternative platform to produce hemagglutinin-based subunit vaccines. This production system provides not only fast and effective response in the context of a pandemic but also enables the supply of big volume vaccines at low cost. Crude plant extracts containing influenza hemagglutinin are considered to use as vaccine sources because of avoidance of related purification steps resulting in low cost production allowing veterinary applications. Highly immunogenic influenza hemagglutinins are urgently required to meet these pre-conditions...
September 20, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28931059/whole-genome-sequencing-of-mutants-with-increased-resistance-against-the-two-peptide-bacteriocin-plantaricin-jk-reveals-a-putative-receptor-and-potential-docking-site
#15
Bie Ekblad, Jon Nissen-Meyer, Tom Kristensen
By whole-genome sequencing of resistant mutants, a putative receptor for plantaricin JK, a two-peptide bacteriocin produced by some Lactobacillus plantarum strains, was identified in Lactobacillus plantarum NCFB 965 and Weissella viridescens NCFB 1655. The receptors of the two species had 66% identical amino acid sequences and belong to the amino acid-polyamine-organocation (APC) transporter protein family. The resistant mutants contained point mutations in the protein-encoding gene resulting in either premature stop codons, leading to truncated versions of the protein, or single amino acid substitutions...
2017: PloS One
https://www.readbyqxmd.com/read/28931053/identification-and-molecular-characterization-of-a-metagenome-derived-l-lysine-decarboxylase-gene-from-subtropical-soil-microorganisms
#16
Jie Deng, Hua Gao, Zhen Gao, Huaxian Zhao, Ying Yang, Qiaofen Wu, Bo Wu, Chengjian Jiang
L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs...
2017: PloS One
https://www.readbyqxmd.com/read/28929019/heterologous-expression-of-plasmodium-vivax-apical-membrane-antigen-1-pvama1-for-binding-peptide-selection
#17
Ching Hoong Chew, Yvonne Ai Lian Lim, Kek Heng Chua
BACKGROUND: Plasmodium is an obligate intracellular parasite. Apical membrane antigen 1 (AMA1) is the most prominent and well characterized malarial surface antigen that is essential for parasite-host cell invasion, i.e., for sporozoite to invade and replicate within hepatocytes in the liver stage and merozoite to penetrate and replicate within erythrocytes in the blood stage. AMA1 has long served as a potent antimalarial drug target and is a pivotal vaccine candidate. A good understanding of the structure and molecular function of this Plasmodium protein, particularly its involvement in host-cell adhesion and invasion, is of great interest and hence it offers an attractive target for the development of novel therapeutics...
2017: PeerJ
https://www.readbyqxmd.com/read/28928040/p-3f-a-microtubule-polymerization-inhibitor-enhances-p53-stability-through-the-change-in-localization-of-rps27a
#18
Huai Wang, Jiang Feng, Tong Zhou, Lijun Wei, Jianming Zhou
Previously, we demonstrated that P-3F, a podophyllum derivative, exhibits a 297-fold enhancement in antitumor activity than VP-16, used as anticancer agent in clinical. The purpose of our present study was to investigate the precise antitumor mechanism action of P-3F. It showed that P-3F inhibited microtubule polymerization in a concentration-dependent manner. The results were in overall agreement with modeling and docking studies performed on P-3F and tubulin. In addition, P-3F increased the levels of P53, this in turn prolonged P53 half-life...
September 16, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28927905/synthesis-pharmacological-activities-and-molecular-docking-studies-of-pyrazolyltriazoles-as-anti-bacterial-and-anti-inflammatory-agents
#19
Cherupally Dayakar, Buddana Sudheer Kumar, Galande Sneha, Gudem Sagarika, Koneru Meghana, Sistla Ramakrishna, Reddy Shetty Prakasham, Bhimapaka China Raju
A series of novel pyrazolyl alcohols (5a-h), pyrazolyl azides (6a-h), and pyrazolyltriazoles (8a-h, 10a-p and 12a-l) were prepared and evaluated for their bioactivity (anti-bacterial and anti-inflammatory) profile. The compound 5c displayed the potent anti-bacterial activity against Micrococcus luteus (MIC 3.9 and MBC 7.81µg/mL). In vitro anti-inflammatory activity data denoted that compound 8b is effective among the tested compounds against IL-6 (IC50 6.23μM). Docking analysis of compounds 5f, 8a-b, 8e-f and 8h displayed high binding energies for the compounds 8a-b and 8h towards TNF-α dimer (2AZ5 protein) and IL-6 (1ALU protein)...
September 15, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28927344/structural-elucidation-of-transmembrane-domain-zero-tmd0-of-ecdl-a-multidrug-resistance-associated-protein-mrp-family-of-atp-binding-cassette-transporter-protein-revealed-by-atomistic-simulation
#20
Krishnendu Bera, Priyanka Rani, Gaurav Kishor, Shikha Agarwal, Antresh Kumar, Durg Vijay Singh
ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known...
September 20, 2017: Journal of Biomolecular Structure & Dynamics
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