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Protein-protein docking

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https://www.readbyqxmd.com/read/28323889/towards-a-critical-evaluation-of-an-empirical-and-volume-based-solvation-function-for-ligand-docking
#1
Heloisa S Muniz, Alessandro S Nascimento
Molecular docking is an important tool for the discovery of new biologically active molecules given that the receptor structure is known. An excellent environment for the development of new methods and improvement of the current methods is being provided by the rapid growth in the number of proteins with known structure. The evaluation of the solvation energies outstands among the challenges for the modeling of the receptor-ligand interactions, especially in the context of molecular docking where a fast, though accurate, evaluation is ought to be achieved...
2017: PloS One
https://www.readbyqxmd.com/read/28323850/ligand-guided-homology-modelling-of-the-gabab2-subunit-of-the-gabab-receptor
#2
Thibaud Freyd, Dawid Warszycki, Stefan Mordalski, Andrzej J Bojarski, Ingebrigt Sylte, Mari Gabrielsen
γ-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system, and disturbances in the GABAergic system have been implicated in numerous neurological and neuropsychiatric diseases. The GABAB receptor is a heterodimeric class C G protein-coupled receptor (GPCR) consisting of GABAB1a/b and GABAB2 subunits. Two GABAB receptor ligand binding sites have been described, namely the orthosteric GABA binding site located in the extracellular GABAB1 Venus fly trap domain and the allosteric binding site found in the GABAB2 transmembrane domain...
2017: PloS One
https://www.readbyqxmd.com/read/28318252/molecular-dynamics-in-mixed-solvents-reveals-protein-ligand-interactions-improves-docking-and-allows-accurate-binding-free-energy-predictions
#3
Juan Pablo Arcon, Lucas A Alfredo Defelipe, Carlos Pablo Modenutti, Elias Daniel Lopez, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A Marti
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Due to its low cost relative to its experimental sibling, Molecular Dynamics (MD) simulations in the presence of different solvent probes mimicking specific type of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28317396/3d-qsar-studies-pharmacophore-modeling-and-virtual-screening-of-diarylpyrazole-benzenesulfonamide-derivatives-as-a-template-to-obtain-new-inhibitors-using-human-carbonic-anhydrase-ii-as-a-model-protein
#4
Yeganeh Entezari Heravi, Hassan Sereshti, Ali Akbar Saboury, Jahan Ghasemi, Marzieh Amirmostofian, Claudiu T Supuran
A 3D-QSAR modeling was performed on a series of diarylpyrazole-benzenesulfonamide derivatives acting as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). The compounds were collected from two datasets with the same scaffold, and utilized as a template for a new pharmacophore model to screen the ZINC database of commercially available derivatives. The datasets were divided into training, test, and validation sets. As the first step, comparative molecular field analysis (CoMFA), CoMFA region focusing and comparative molecular similarity indices analysis (CoMSIA) in parallel with docking studies were applied to a set of 41 human (h) CA II inhibitors...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28315331/sublethal-doses-of-neonicotinoid-imidacloprid-can-interact-with-honey-bee-chemosensory-protein-1-csp1-and-inhibit-its-function
#5
Hongliang Li, Jing Tan, Xinmi Song, Fan Wu, Mingzhu Tang, Qiyun Hua, Huoqing Zheng, Fuliang Hu
As a frequently used neonicotinoid insecticide, imidacloprid can impair the chemoreceptive behavior of honey bees even at sublethal doses, while the physiochemical mechanism has not been further revealed. Here, multiple fluorescence spectra, thermodynamic method, and molecular docking were used to study the interaction and the functional inhibition of imidacloprid to the recombinant CSP1 protein in Asian honey bee, Apis cerana. The results showed that the fluorescence intensity (λem = 332 nm) of CSP1 could be significantly quenched by imidacloprid in a dynamic mode...
March 14, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28314775/insights-into-rad3-kinase-recruitment-from-the-crystal-structure-of-the-dna-damage-checkpoint-protein-rad26
#6
Kasper Røjkjær Andersen
Metabolic products and environmental factors constantly damage DNA. To protect against these insults and maintain genome integrity, cells have evolved mechanisms to repair DNA lesions. One such mechanism involves Rad3, a master kinase coordinating the DNA damage response. Rad26 is a functional subunit of the Rad3-Rad26 complex and responsible for bringing the kinase to sites of DNA damage. Here, I present the crystal structure of Rad26 and identify the elements important for recruiting Rad3. The structure suggests that Rad26 is a dimer with a conserved interface in the N-terminal part of the protein...
March 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28314478/osteoinductive-effects-of-glyceollins-on-adult-mesenchymal-stromal-stem-cells-from-adipose-tissue-and-bone-marrow
#7
Marjorie E Bateman, Amy L Strong, Ryan S Hunter, Melyssa R Bratton, Rajesh Komati, Jayalakshmi Sridhar, Kevin E Riley, Guangdi Wang, Daniel J Hayes, Stephen M Boue, Matthew E Burow, Bruce A Bunnell
BACKGROUND: While current therapies for osteoporosis focus on reducing bone resorption, the development of therapies to regenerate bone may also be beneficial. Promising anabolic therapy candidates include phytoestrogens, such as daidzein, which effectively induce osteogenesis of adipose-derived stromal cells (ASCs) and bone marrow stromal cells (BMSCs). PURPOSE: To investigate the effects of glyceollins, structural derivatives of daidzein, on osteogenesis of ASCs and BMSCs...
April 15, 2017: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/28314116/secretory-proteome-analysis-of-streptomycin-resistant-mycobacterium-tuberculosis-clinical-isolates
#8
Divakar Sharma, Deepa Bisht
Tuberculosis still remains one of the most fatal infectious diseases. Streptomycin (SM) is the drug of choice, especially for patients with multidrug-resistant tuberculosis or category II patients, because it targets the protein synthesis machinery by interacting with steps of translation. Several mechanisms have been proposed to explain the resistance, but our knowledge is inadequate. Secretome often plays an important role in pathogenesis and is considered an attractive reservoir for the development of novel diagnostic markers and targets...
March 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28306713/trypanocidal-effect-of-isotretinoin-through-the-inhibition-of-polyamine-and-amino-acid-transporters-in-trypanosoma-cruzi
#9
Chantal Reigada, Edward A Valera-Vera, Melisa Sayé, Andrea E Errasti, Carla C Avila, Mariana R Miranda, Claudio A Pereira
Polyamines are essential compounds to all living organisms and in the specific case of Trypanosoma cruzi, the causative agent of Chagas disease, they are exclusively obtained through transport processes since this parasite is auxotrophic for polyamines. Previous works reported that retinol acetate inhibits Leishmania growth and decreases its intracellular polyamine concentration. The present work describes a combined strategy of drug repositioning by virtual screening followed by in vitro assays to find drugs able to inhibit TcPAT12, the only polyamine transporter described in T...
March 17, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28306255/development-of-potent-and-selective-antagonists-for-the-utp-activated-p2y4-receptor
#10
Muhammad Rafehi, Enas Malik, Alexander Neumann, Aliaa Abdelrahman, Theodor Hanck, Vigneshwaran Namasivayam, Christa E Müller, Younis Baqi
P2Y4 is a Gq protein-coupled receptor activated by uridine-5'-triphosphate (UTP), which is widely expressed in the body, e.g., in intestine, heart, and brain. No selective P2Y4 receptor antagonist has been described so far. Therefore, we developed and optimized P2Y4 antagonists based on an anthraquinone scaffold. Potency was assessed by a fluorescence-based assay measuring inhibition of UTP-induced intracellular calcium release in 1321N1 astrocytoma cells stably transfected with the human P2Y4 receptor. The most potent compound of the present series, sodium 1-amino-4-[4-(2,4-dimethylphenylthio)phenylamino]-9,10-dioxo-9,10-dihydroanthracene-2-sulfonate (PSB-16133, 61) exhibited an IC50 value of 233 nM, selectivity versus other P2Y receptor subtypes, and is thought to act as an allosteric antagonist...
March 17, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28303164/adverse-drug-reactions-triggered-by-the-common-hla-b-57-01-variant-a-molecular-docking-study
#11
George Van Den Driessche, Denis Fourches
BACKGROUND: Human leukocyte antigen (HLA) surface proteins are directly involved in idiosyncratic adverse drug reactions. Herein, we present a structure-based analysis of the common HLA-B*57:01 variant known to be responsible for several HLA-linked adverse effects such as the abacavir hypersensitivity syndrome. METHODS: First, we analyzed three X-ray crystal structures involving the HLA-B*57:01 protein variant, the anti-HIV drug abacavir, and different co-binding peptides present in the antigen-binding cleft...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28300085/the-scaffold-protein-p140cap-limits-erbb2-mediated-breast-cancer-progression-interfering-with-rac-gtpase-controlled-circuitries
#12
Silvia Grasso, Jennifer Chapelle, Vincenzo Salemme, Simona Aramu, Isabella Russo, Nicoletta Vitale, Ludovica Verdun di Cantogno, Katiuscia Dallaglio, Isabella Castellano, Augusto Amici, Giorgia Centonze, Nanaocha Sharma, Serena Lunardi, Sara Cabodi, Federica Cavallo, Alessia Lamolinara, Lorenzo Stramucci, Enrico Moiso, Paolo Provero, Adriana Albini, Anna Sapino, Johan Staaf, Pier Paolo Di Fiore, Giovanni Bertalot, Salvatore Pece, Daniela Tosoni, Stefano Confalonieri, Manuela Iezzi, Paola Di Stefano, Emilia Turco, Paola Defilippi
The docking protein p140Cap negatively regulates tumour cell features. Its relevance on breast cancer patient survival, as well as its ability to counteract relevant cancer signalling pathways, are not fully understood. Here we report that in patients with ERBB2-amplified breast cancer, a p140Cap-positive status associates with a significantly lower probability of developing a distant event, and a clear difference in survival. p140Cap dampens ERBB2-positive tumour cell progression, impairing tumour onset and growth in the NeuT mouse model, and counteracting epithelial mesenchymal transition, resulting in decreased metastasis formation...
March 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28299743/computational-approaches-to-matrix-metalloprotease-drug-design
#13
Tanya Singh, B Jayaram, Olayiwola Adedotun Adekoya
Matrix metalloproteinases (MMPs) are a family of zinc-containing enzymes required for homeostasis. These enzymes are an important class of drug targets as their over expression is associated with many disease states. Most of the inhibitors reported against this class of proteins have failed in clinical trials due to lack of specificity. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising, (1) docking of small molecule inhibitors against the target MMPs, (2) derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, (3) molecular dynamics simulations on the docked ligand-MMP complexes, and (4) evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28299584/combined-molecular-docking-and-qsar-study-of-fused-heterocyclic-herbicide-inhibitors-of-d1-protein-in-photosystem-ii-of-plants
#14
Simona Funar-Timofei, Ana Borota, Luminita Crisan
Cinnoline, pyridine, pyrimidine, and triazine herbicides were found be inhibitors of the D1 protein in photosystem II (D1 PSII) electron transport of plants. The photosystem II inhibitory activity of these herbicides, expressed by experimental [Formula: see text] values, was modeled by a docking and quantitative structure-activity relationships study. A conformer ensemble for each of the herbicide structure was generated using the MMFF94s force field. These conformers were further employed in a docking approach, which provided new information about the rational "active conformations" and various interaction patterns of the herbicide derivatives with D1 PSII...
March 16, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28299519/insights-into-the-effects-of-glycosylation-and-the-monosaccharide-binding-activity-of-the-plant-lectin-cratabl
#15
Laercio Pol-Fachin
CrataBL is a glycoprotein isolated from Crataeva tapia bark, containing two N-glycosylation sites. It has been identified to present lectin activity with some specificity for binding glucose over galactose. However, to date, no information on the effects of glycosylation or CrataBL monosaccharide-binding sites and monosaccharide specificity has been obtained. Thus, molecular docking and molecular dynamics simulations were employed to characterize the glycosylated CrataBL conformation and dynamics in aqueous solutions, as well as the molecular basis for its binding specificity...
March 15, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28298217/large-scale-gene-network-analysis-reveals-the-significance-of-extracellular-matrix-pathway-and-homeobox-genes-in-acute-myeloid-leukemia-an-introduction-to-the-pigengene-package-and-its-applications
#16
Amir Foroushani, Rupesh Agrahari, Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan, Habil Zare
BACKGROUND: The distinct types of hematological malignancies have different biological mechanisms and prognoses. For instance, myelodysplastic syndrome (MDS) is generally indolent and low risk; however, it may transform into acute myeloid leukemia (AML), which is much more aggressive. METHODS: We develop a novel network analysis approach that uses expression of eigengenes to delineate the biological differences between these two diseases. RESULTS: We find that specific genes in the extracellular matrix pathway are underexpressed in AML...
March 16, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28296270/analogues-of-dehydroacetic-acid-as-selective-and-potent-agonists-of-an-ectopic-odorant-receptor-through-a-combination-of-hydrophilic-and-hydrophobic-interactions
#17
Bernie Byunghoon Park, NaHye Lee, YunHye Kim, YoonGyu Jae, Seunghyun Choi, NaNa Kang, Yu Ri Hong, Kiwon Ok, Jeonghee Cho, Young Ho Jeon, Eun Hee Lee, Youngjoo Byun, JaeHyung Koo
Identification of potent agonists of odorant receptors (ORs), a major class of G protein-coupled receptors, remains challenging due to complex receptor-ligand interactions. ORs are present in both olfactory and non-chemosensory tissues, indicating roles beyond odor detection that may include modulating physiological functions in non-olfactory tissues. Selective and potent agonists specific for particular ORs can be used to investigate physiological functions of ORs in non-chemosensory tissues. In this study, we designed and synthesized novel synthetic dehydroacetic acid analogues as agonists of odorant receptor 895 (Olfr895) expressed in bladder...
March 15, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28295815/elucidating-the-interaction-of-clofazimine-with-bovine-liver-catalase-a-comprehensive-spectroscopic-and-molecular-docking-approach
#18
Masihuz Zaman, Saima Nusrat, Syed Mohammad Zakariya, Mohsin Vahid Khan, Mohammad Rehan Ajmal, Rizwan Hasan Khan
Nowadays, understanding of interface between protein and drugs has become an active research area of interest. These types of interactions provide structural guidelines in drug design with greater clinical efficacy. Thus, structural changes in catalase induced by clofazimine were monitored by various biophysical techniques including UV-visible spectrometer, fluorescence spectroscopy, circular dichroism, and dynamic light scattering techniques. Increase in absorption spectra (UV-visible spectrum) confers the complex formation between drug and protein...
March 14, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28295743/characterization-of-surface-binding-sites-in-glycoside-hydrolases-a-computational-study
#19
Samaneh Samaei-Daryan, Bahram Goliaei, Azadeh Ebrahim-Habibi
Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty-five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut-off differences in each SBSs with different ligand size, molecular docking were performed...
March 15, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28295323/crip1a-inhibits-endocytosis-of-g-protein-coupled-receptors-activated-by-endocannabinoids-and-glutamate-by-a-common-molecular-mechanism
#20
Fabrizio Mascia, Lisa Klotz, Judith Lerch, Mostafa A Ahmed, Yan Zhang, Ralf Enz
The excitability of the central nervous system depends largely on the surface density of neurotransmitter receptors. The endocannabinoid receptor CB1 R and the metabotropic glutamate receptor mGlu8 R are expressed presynaptically where they reduce glutamate release into the synaptic cleft. Recently, the CB1 R interacting protein CRIP1a was identified and characterized to regulate CB1 R activity in neurons. However, underlying molecular mechanisms are largely unknown. Here, we identified a common mechanism used by CRIP1a to regulate the cell surface density of two different types of G-protein coupled receptors, CB1 R and mGlu8a R...
March 15, 2017: Journal of Neurochemistry
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