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Molecular docking

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https://www.readbyqxmd.com/read/28734977/modulation-of-the-interaction-between-human-p450-3a4-and-b-megaterium-reductase-via-engineered-loops
#1
Silvia Castrignanò, Serena D'Avino, Giovanna Di Nardo, Gianluca Catucci, Sheila J Sadeghi, Gianfranco Gilardi
Chimerogenesis involving cytochromes P450 is a successful approach to generate catalytically self-sufficient enzymes. However, the connection between the different functional modules should allow a certain degree of flexibility in order to obtain functional and catalytically efficient proteins. We previously applied the molecular Lego approach to develop a chimeric P450 3A4 enzyme linked to the reductase domain of P450 BM3 (BMR). Three constructs were designed with the connecting loop containing no glycine, 3 glycine or 5 glycine residues and showed a different catalytic activity and coupling efficiency...
July 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28734777/inhibitor-mechanisms-in-the-s1-binding-site-of-the-dopamine-transporter-defined-by-multi-site-molecular-tethering-of-photoactive-cocaine-analogs
#2
Danielle Krout, Akula Bala Pramod, Rejwi Acharya Dahal, Michael J Tomlinson, Babita Sharma, James D Foster, Mu-Fa Zou, Comfort Boatang, Amy Hauck Newman, John R Lever, Roxanne A Vaughan, L Keith Henry
Dopamine transporter (DAT) blockers like cocaine and many other abused and therapeutic drugs bind and stabilize an inactive form of the transporter inhibiting reuptake of extracellular dopamine (DA). The resulting increases in DA lead to the ability of these drugs to induce psychomotor alterations and addiction, but paradoxical findings in animal models indicate that not all DAT antagonists induce cocaine-like behavioral outcomes. How this occurs is not known, but one possibility is that uptake inhibitors may bind at multiple locations or in different poses to stabilize distinct conformational transporter states associated with differential neurochemical endpoints...
July 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28734645/computational-study-of-the-competitive-binding-of-valproic-acid-glucuronide-and-carbapenem-antibiotics-to-acylpeptide-hydrolase
#3
Takeshi Ishikawa, Hiroki Otaki, Satoshi Mizuta, Masami Kuriyama, Osamu Onomura, Norihide Higuchi, Mihoko N Nakashima, Mikiro Nakashima, Kaname Ohyama
The efficacy of the antiepileptic drug VPA is decreased by co-administered carbapenems (CBPMs). The mechanism of CBPM selective inhibition of acylpeptide hydrolase (APEH) hydrolysis of VPA-glucuronide (VPA-G) to VPA is unclear due to the lack of APEH structural information. Here we performed homology modeling of the three-dimensional structure of APEH and subsequent docking simulations with a modeled structure to understand this mechanism. Docking simulations indicated that four groups of binding structures were involved in the binding of VPA-G, panipenem, and meropenem to APEH, but only one or two binding structures were involved in the binding of meropenem with an open β-lactam ring structure and other antibiotics involving ampicillin...
April 30, 2017: Drug Metabolism and Pharmacokinetics
https://www.readbyqxmd.com/read/28733815/structure-of-isolated-z-disks-from-honeybee-flight-muscle
#4
Mara Rusu, Zhongjun Hu, Kenneth A Taylor, John Trinick
The Z-disk is a complex structure comprising some 40 proteins that are involved in the transmission of force developed during muscle contraction and in important signalling pathways that govern muscle homeostasis. In the Z-disk the ends of antiparallel thin filaments from adjacent sarcomeres are crosslinked by α-actinin. The structure of the Z-disk lattice varies greatly throughout the animal kingdom. In vertebrates the thin filaments form a tetragonal lattice, whereas invertebrate flight muscle has a hexagonal lattice...
July 21, 2017: Journal of Muscle Research and Cell Motility
https://www.readbyqxmd.com/read/28733707/angiotensin-ii-type-1-receptor-blockers-inhibit-kat-ii-activity-in-the-brain-its-possible-clinical-applications
#5
Izabela Zakrocka, Katarzyna M Targowska-Duda, Artur Wnorowski, Tomasz Kocki, Krzysztof Jóźwiak, Waldemar A Turski
Angiotensin II receptor blockers (ARBs) are one of the most frequently recommended antihypertensive drugs. Apart from their activity towards the circulatory system, ARBs also penetrate the blood-brain barrier and display neuroprotective effects. Kynurenic acid (KYNA) is an endogenous metabolite of tryptophan produced by kynurenine aminotransferase II (KAT II) in the brain. Antagonism towards all ionotropic glutamate (GLU) receptors is the main mechanism of KYNA action. An elevated brain level of KYNA is linked with memory impairment and psychotic symptoms...
July 21, 2017: Neurotoxicity Research
https://www.readbyqxmd.com/read/28732283/deciphering-the-mechanism-of-interaction-of-edifenphos-with-calf-thymus-dna
#6
Ajaz Ahmad, Masood Ahmad
Edifenphos is an important organophosphate pesticide with many antifungal and anti-insecticidal properties but it may cause potential hazards to human health. In this work, we have tried to explore the binding mode of action and mechanism of edifenphos to calf thymus DNA (CT-DNA). Several experiments such as ultraviolet-visible absorption spectra and emission spectroscopy showed complex formation between edifenphos and CT-DNA and low binding constant values supporting groove binding mode. These results were further confirmed by circular dichroism (CD), CT-DNA melting studies, viscosity measurements, density functional theory and molecular docking...
July 13, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28732041/understanding-russell-s-viper-venom-factor-v-activator-s-substrate-specificity-by-surface-plasmon-resonance-and-in-silico-studies
#7
Pradeep K Yadav, Christian B Antonyraj, Syed Ibrahim Basheer Ahamed, Sistla Srinivas
Blood coagulation factor V (FV) is activated either by Factor X or thrombin, cleaving at three different sites viz., Site I (Arg709-Ser710), site II (Arg1018-Thr1019), and site III (Arg1545-Ser1546). Russell's viper venom factor V activator (RVV-V) is a thrombin-like serine proteinase that activates FV with selective, single cleavage at site III. A long lasting effort is being pending in understanding the 'selective' binding specificity of the RVV-V towards site III. Here, we present the binding kinetic study of RVV-V with two designed peptides corresponding to the regions from site I (Gln699-Asn713) and site II (1008Lys-Pro1022), respectively, that include 15 amino acids...
2017: PloS One
https://www.readbyqxmd.com/read/28730429/a-new-method-to-predict-ion-effects-in-rna-folding
#8
Li-Zhen Sun, Shi-Jie Chen
The strong interaction between metal ions in solution and highly charged RNA molecules is critical for RNA structure formation and stabilization. Metal ions binding to RNA can induce RNA structural changes that are important for RNA cellular functions. Therefore, quantitative modeling of the ion effects is essential for RNA structure prediction and RNA-based molecular design. Recently, inspired by the increasing experimental evidence that supports the importance of ion correlation and fluctuation in ion-RNA interactions, we developed a new computational model, Monte Carlo Tightly Bound Ion (MCTBI) model...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729760/structural-insight-into-the-binding-of-c60-derivatives-with-enoyl-pyruvate-transferase-from-helicobacter-pylori
#9
Mohammad Teimouri, Muhammad Junaid, Abbas Khan, Houjin Zhang
Helicobacter pylori (H. pylori) is a human pathogen associated with acute gastritis and peptic ulcer. The MurA enzyme is an important drug target for the identification of ligands with improved efficacy and acceptable pharmaco-kinetic properties. We developed a homology model of H. Pylori MurA followed by refinement and molecular dynamics (MD) simulations. A total of 16 C60-derivatives were docked and its docking score were compared. Some of the known inhibitors were also similarly characterized and compared...
2017: Bioinformation
https://www.readbyqxmd.com/read/28729623/3d-qsar-studies-on-maslinic-acid-analogs-for-anticancer-activity-against-breast-cancer-cell-line-mcf-7
#10
Sarfaraz Alam, Feroz Khan
Global prevalence of breast cancer and its rising frequency makes it a key area of research in drug discovery programs. The research article describes the development of field based 3D-QSAR model based on human breast cancer cell line MCF7 in vitro anticancer activity, which defines the molecular level understanding and regions of structure-activity relationship for triterpene maslinic acid and its analogs. The key features such as average shape, hydrophobic regions and electrostatic patterns of active compounds were mined and mapped to virtually screen potential analogs...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729227/computational-and-experimental-prediction-of-molecules-involved-in-the-anti-melanoma-action-of-berberine
#11
Bin Liu, Xiu-Qiong Fu, Ting Li, Tao Su, Hui Guo, Pei-Li Zhu, Anfernee Kai-Wing Tse, Shi-Ming Liu, Zhi-Ling Yu
ETHNOPHARMACOLOGIC RELEVANCE: Berberine (BBR) is a naturally occurring alkaloid compound that can be found in Chinese medicinal herbs such as Rhizoma Coptidis and Phellodendri Cortex. These BBR containing herbs are commonly used by Chinese medicine doctors to treat cancers including melanoma. In this study, we explored proteins potentially involved in the anti-melanoma effects of BBR using an integrative computational and experimental approach. MATERIALS AND METHODS: Target proteins of BBR were predicted using the reverse pharmacophore screening, molecular docking and molecular dynamics...
July 17, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28728523/structural-insights-into-the-binding-of-small-ligand-molecules-to-a-g-quadruplex-dna-located-in-the-hiv-1-promoter
#12
Petar M Mitrasinovic
Targeting guanine (G)-rich DNA sequences, folded into non-canonical G-quadruplex (G4) structures, by small ligand molecules is a promising strategy for gene therapy of various diseases. There is experimental proposal that, among eight studied ligands, nitidine chloride - NC and a benzo phenanthridine derivative - BPD have the highest binding affinities for such a sequence (5'-T(1)G(2)G(3)C(4)C(5)T(6)G(7)G(8)G(9)C(10)G(11)G(12)G(13)A(14)C(15)T(16)G(17)G(18)G(19)-3') in the HIV-1 promoter, indicating that an anti-HIV-1 prodrug may regulate the expression of the promoter...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28728517/using-molecular-dynamics-for-the-refinement-of-atomistic-models-of-gpcrs-by-homology-modeling
#13
Cecylia S Lupala, Bahareh Rasaeifar, Patricia Gomez-Gutierrez, Juan J Perez
Despite GPCRs share a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs is steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modelling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28728106/multipotent-ache-and-bace-1-inhibitors-for-the-treatment-of-alzheimer-s-disease-design-synthesis-and-bio-analysis-of-7-amino-1-4-dihydro-2h-isoquilin-3-one-derivates
#14
Xiong-Jie Zhao, Da-Min Gong, Yu-Ren Jiang, Dong Guo, Yao Zhu, You-Chao Deng
In this paper, the preparation of a new class of multi-target-directed ligands (MTDLs) based on a 7-amino-1,4-dihydro-2H-isoquilin-3-one, whose lead (compound I) showed promising properties in acetylcholinesterase (AChE) inhibitory activity [1], is described. The results of in vitro activities and molecular docking demonstrated that the target molecule (compounds 10a-n) with three parts of aromatic moieties and appropriate structural length can interact with aromatic residues in catalytic active site (CAS), peripheral anionic site (PAS) and the channel of AChE...
July 5, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28728105/discovery-of-imidazopyridines-containing-isoindoline-1-3-dione-framework-as-a-new-class-of-bace1-inhibitors-design-synthesis-and-sar-analysis
#15
Sara Azimi, Afsaneh Zonouzi, Omidreza Firuzi, Aida Iraji, Mina Saeedi, Mohammad Mahdavi, Najmeh Edraki
Alzheimer's disease is characterized by chronic neurodegeneration leading to dementia. The main cause of neurodegeneration is considered to be the accumulation of amyloid-β. Inhibiting BACE1 is a well-studied approach to lower the burden of amyloid-β aggregates. We designed a series of imidazopyridines-based compounds bearing phthalimide moieties as inhibitors of BACE1. The compounds 8a-o were synthesized by the Groebke-Blackburn-Bienaymé three-component reaction of heteroaromatic amidines, aldehydes and isocyanides...
June 24, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28728041/multi-structure-docking-analysis-of-bace1-crystal-structures-and-non-peptidic-ligands
#16
Zahra Haghighijoo, Bahram Hemmateenejad, Najmeh Edraki, Ramin Miri, Saeed Emami
In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands' structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis...
June 28, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28727189/inversion-of-cpadh5-enantiopreference-and-altered-chain-length-specificity-for-methyl-3-hydroxyalkanoates
#17
Yunus Ensari, Gaurao V Dhoke, Mehdi D Davari, Marco Bocola, Anna Joelle Ruff, Ulrich Schwaneberg
Expanding the substrate scope of enzymes opens up new routes for synthesis of valuable chemicals. Ketone-functionalized fatty acid derivatives and corresponding chiral alcohols are valuable building blocks for the synthesis of a variety of chemicals including pharmaceuticals. The alcohol dehydrogenase from Candida parapsilosis (cpADH5) catalyzes the reversible oxidations of chiral alcohols and has a broad substrate range; a challenge for cpADH5 is to convert alcohols with small substituents (methyl or ethyl) next to the oxidized alcohol moiety...
July 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28726760/synthesis-antitumor-evaluation-and-molecular-docking-of-new-morpholine-based-heterocycles
#18
Zeinab A Muhammad, Mastoura M Edrees, Rasha A M Faty, Sobhi M Gomha, Seham S Alterary, Yahia N Mabkhot
A series of new morpholinylchalcones was prepared and then used as building blocks for constructing a series of 7-morpholino-2-thioxo-2,3-dihydropyrido[2,3-d]pyrimidin-4(1H)-ones via their reaction with 6-aminothiouracil. The latter thiones reacted with the appropriate hydrazonoyl chloride to give the corresponding pyrido[2,3-d][1,2,4]triazolo[4,3-a]pyrimidin-5(1H)-ones. The assigned structures for all the newly synthesized compounds were confirmed on the basis of elemental analyses and spectral data and the mechanisms of their formation were also discussed...
July 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28726400/quinoliniumolate-and-2h-1-2-3-triazole-derivatives-from-the-stems-of-paramignya-trimera-and-their-%C3%AE-glucosidase-inhibitory-activities-in-vitro-and-in-silico-studies
#19
Nhan T Nguyen, Phu H Dang, Ngoc X T Vu, Tho H Le, Mai T T Nguyen
From a CHCl3-soluble extract of the stems of Paramignya trimera, two new alkaloids, (E)-2-(prop-1-enyl)-N-methylquinolinium-4-olate (1) and (R)-2-ethylhexyl 2H-1,2,3-triazole-4-carboxylate (2), were isolated. Their structures were elucidated based on the spectroscopic data interpretation. Compound 2 possesses α-glucosidase inhibitory activity, with an IC50 value of 137.9 μM. Molecular docking studies of 1 and 2 with human maltase-glucoamylase (MGAM) were performed for the first time; thus, the 2,3-diH(+)-1H-1,2,3-triazolium cation (2i) showed good interactions with both MGAM-N (2QMJ) and -C (3TOP) terminal subunits...
July 20, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28726171/qsar-modeling-docking-and-admet-studies-for-exploration-of-potential-anti-malarial-compounds-against-plasmodium-falciparum
#20
Tabish Qidwai
Development of resistance in the Plasmodium falciparum to Artemisinin, the most effective anti-malarial compound, threatens malaria elimination tactics. To gain more efficacious Artemisinin derivatives, QSAR modeling and docking was performed. In the present study, 2D-QSAR model and molecular docking were used to evaluate the Artemisinin compounds and to reveal their binding modes and structural basis of inhibitory activity. Moreover, ADMET-related descriptors have been calculated to predict the pharmacokinetic properties of the effective compounds...
December 2016: In Silico Pharmacology
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