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Molecular docking

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https://www.readbyqxmd.com/read/29778043/investigation-of-interactions-of-comtan-with-human-serum-albumin-by-mathematically-modeled-voltammetric-data-a-study-from-bio-interaction-to-biosensing
#1
Ali R Jalalvand, Sirous Ghobadi, Hector C Goicoechea, Hui-Wen Gu, Esmael Sanchooli
In this work, voltammetric data recorded at a glassy carbon electrode (GCE) were separately used to investigate the interactions of entacapone (Comtan, CAT) with human serum albumin (HSA). Then, an augmented data matrix was constructed by the combination of voltammetric and spectroscopic data and simultaneously analysed by multivariate curve resolution-alternating least squares (MCR-ALS) to obtain more information about CAT-HSA interactions. The absence of rotational ambiguities in results obtained by MCR-ALS was verified with the help of MCR-BANDS and we confirmed that the results were unambiguous and reliable...
May 16, 2018: Bioelectrochemistry
https://www.readbyqxmd.com/read/29777941/characterization-of-the-binding-of-a-novel-antitumor-drug-ibrutinib-with-human-serum-albumin-insights-from-spectroscopic-calorimetric-and-docking-studies
#2
Bin Tang, Peixiao Tang, Jiawei He, Hongqin Yang, Hui Li
Ibrutinib (IBR) is a novel Bruton's tyrosine kinase inhibitor and shows good efficacy for several B-cell malignancies. In the current study, the molecular mechanism of the interaction between IBR and the transport protein human serum albumin (HSA) was ascertained by spectroscopic, calorimetric, and docking studies. Detailed investigations on affinity parameter, binding model, conformational change, and site selectivity were implemented by receptor-based and ligand-based analysis. An unusual fluorescence co-quenching (mutual quenching) was observed in the binding of IBR to HSA, followed by a static mechanism...
May 16, 2018: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/29777928/binding-studies-of-triclocarban-with-bovine-serum-albumin-insights-from-multi-spectroscopy-and-molecular-modeling-methods
#3
Jiao Guan, Xin Yan, Yajing Zhao, Yinhe Sun, Xin Peng
The antimicrobial triclocarban (TCC) is frequently found in various personal care products (PCPs), and recent studies have demonstrated that it shows a high unintended biological activity on humans and wildlife. To evaluate the toxicity of TCC at the protein level, the effect of TCC on bovine serum albumin (BSA) has been investigated using various spectroscopic methods in combination with molecular modeling. Analysis of fluorescence quenching data of BSA revealed the formation of a ground state BSA-TCC complex with a binding constant of 2...
May 9, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29777900/material-basis-research-for-huangqi-jianzhong-tang-against-chronic-atrophic-gastritis-rats-through-integration-of-urinary-metabonomics-and-systemsdock
#4
Yuetao Liu, Wenqian Xu, GuoHong Wang, Xuemei Qin
ETHNOPHARMACOLOGICAL RELEVANCE: Huangqi Jianzhong Tang (HQJZ), a celebrated traditional Chinese medicine (TCM), is commonly used for treatment of chronic atrophic gastritis (CAG) in China. AIM OF THE STUDY: We aimed to screen out the material basis of HQJZ against CAG. MATERIALS AND METHODS: CAG rat model was constructed by alternant administrations of ammonia solution and sodium deoxycholate, and the hunger disorder method. Body weight, biochemical indexes and histopathological exam were used to evaluate the efficacy of HQJZ...
May 16, 2018: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29777812/exploring-the-intermolecular-interactions-and-contrasting-binding-of-flufenamic-acid-with-hemoglobin-and-lysozyme-a-biophysical-and-docking-insight
#5
Sameer Shakeel Ansari, Imtiyaz Yousuf, Farukh Arjmand, Mohammad Khursheed Siddiqi, Saeeda Naqvi
The intermolecular interaction of flufenamic acid (Hfluf) with two model proteins i.e., hemoglobin and lysozyme was explored using fluorescence, UV-vis, circular dichroism, DLS, and molecular docking techniques. The corroborative spectroscopic techniques suggested efficient binding of Hfluf to both the proteins. The S-V plot in Hb-Hfluf system showed positive deviation highlighting the presence of both static and dynamic quenching. Hence, ground state complex model and sphere of action quenching model were used for the study...
May 16, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29777803/an-isolate-of-potato-virus-x-capsid-protein-from-n-benthamiana-insights-from-homology-modeling-and-molecular-dynamics-simulation
#6
Neda Esfandiari, Yahya Sefidbakht
Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood. SDS-PAGE, ELISA, Western blot and RT-PCR molecular examinations were performed on the inoculated plants Nicotiana benthamiana. The pathological symptoms were related to the PVX isolate...
May 16, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29777686/molecular-interactions-between-geobacter-sulfurreducens-triheme-cytochromes-and-the-redox-active-analogue-for-humic-substances
#7
Joana M Dantas, Marisa R Ferreira, Teresa Catarino, Oleksandr Kokhan, P Raj Pokkuluri, Carlos A Salgueiro
The bacterium Geobacter sulfurreducens can transfer electrons to the quinone moieties of humic substances or to anthraquinone-2,6-disulfonate (AQDS), a model for the humic acids. The reduced form of AQDS (AH2 QDS) can also be used as energy source G. sulfurreducens. Such bi-directional utilization of humic substances confers competitive advantages to these bacteria in Fe(III) enriched environments. Previous studies have shown that the triheme cytochrome PpcA from G. sulfurreducens has a bi-functional behavior toward the humic substance analogue...
May 16, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29777335/a-trisubstituted-pyrazole-derivative-reduces-dmba-induced-mammary-tumor-growth-in-rats-by-inhibiting-estrogen-receptor-%C3%AE-expression
#8
Hanumappa Ananda, Kothanahally S Sharath Kumar, Muddenahalli S Sudhanva, Shobith Rangappa, Kanchugarakoppal S Rangappa
Aberrant expression of estrogen receptor alpha (ER-α) is observed in many pathological complications like breast cancer, endometrial cancer, and in osteoporosis. ER-α plays a vital role in the initiation and progression of breast cancer and confers chemo and radioresistance to the cancer cells by upregulating expression of anti-apoptotic proteins. The synthetic pyrazole derivative 3-(1-(4-bromophenyl)-5-phenyl-1H-pyrazol-3-yl)pyridine (compound 5d) displays significant cytotoxicity against mammary carcinoma cells...
May 18, 2018: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29776833/novel-oxazolxanthone-derivatives-as-a-new-type-of-%C3%AE-glucosidase-inhibitor-synthesis-activities-inhibitory-modes-and-synergetic-effect
#9
Sen-Miao Ding, Tian Lan, Gao-Jie Ye, Jia-Jun Huang, You Hu, Yi-Ran Zhu, Bo Wang
Xanthone derivatives have shown good α-glucosidase inhibitory activity and have drawn increased attention as potential anti-diabetic compounds. In this study, a series of novel oxazolxanthones were designed, synthesized, and investigated as α-glucosidase inhibitors. Inhibition assays indicated that compounds 4-21 bearing oxazole rings exhibited up to 30-fold greater inhibitory activity compared to their corresponding parent compound 1b. Among them, compounds 5-21 (IC50  = 6.3 ± 0.4-38.5 ± 4...
May 15, 2018: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29775968/in-silico-structure-prediction-and-inhibition-mechanism-studies-of-athda14-as-revealed-by-homology-modeling-docking-molecular-dynamics-simulation
#10
Ming-Lang Zhao, Wang Wang, Hu Nie, Sha-Sha Cao, Lin-Fang Du
Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots...
May 6, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29775950/drechmerin-h-a-novel-1-2-2-18-diseco-indole-diterpenoid-from-the-fungus-drechmeria-sp-as-a-natural-agonist-of-human-pregnane-x-receptor
#11
Jian-Chao Zhao, Zhi-Lin Luan, Jia-Hao Liang, Zhong-Bin Cheng, Cheng-Peng Sun, Ya-Li Wang, Meng-Yue Zhang, Tian-Yuan Zhang, Yong Wang, Tian-Mei Yang, Ying-Ying Wu, Yi-Xuan Zhang, Xin-Yu Zhao, Xiao-Chi Ma
A novel 1(2), 2(18)-diseco indole diterpenoid, drechmerin H (1), was isolated from the fermentation broth of Drechmeria sp. together with a new indole diterpenoid, 2'-epi terpendole A (3), and a known analogue, terpendole A (2). Their structures were determined by HRESIMS, 1D and 2D NMR, ECD, and X-ray single crystal diffraction analyses as well as quantum chemical calculation. The abosulte configuration of terpendole A (2) was determined for the first time. Compound 1 displayed the significant agonistic effect on pregnane X receptor (PXR) with EC50 value of 134...
May 9, 2018: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29775804/in-silico-study-of-the-active-site-of-helicobacter-pylori-urease-and-its-inhibition-by-hydroxamic-acids
#12
Richa Arora, Upasana Issar, Rita Kakkar
Hydroxamic acids have emerged as the most promising candidates from among the different classes of inhibitors of urease. In order to understand the mechanism of their action, we have studied in detail using quantum mechanics the active site of Helicobacter pylori urease complexed with acetohydroxamic acid. A diverse library of ligands having the hydroxamate moiety has been prepared and docked into the active site of urease using the QM/MM methodology. It is found that hydroxamic acids with hydrophobic groups attached to them are more potent inhibitors of urease because they can easily penetrate the hydrophobic environment surrounding the active site...
May 1, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29775777/antidepressant-potential-of-novel-flavonoids-derivatives-from-sweet-violet-viola-odorata-l-pharmacological-biochemical-and-computational-evidences-for-possible-involvement-of-serotonergic-mechanism
#13
Nasiara Karim, Imran Khan, Abeer Abdelhalim, Ajmal Khan, Sobia Ahsan Halim
Plant-derived natural constituents are of great interest in modern drug discovery due to their natural diversity. Viola odorata L has been traditionally used for the treatment of neuropsychiatric disorders. The present study was undertaken to isolate phytoconstituents including three flavonoids 5,7-Dihydroxy-3,6-dimethoxyflavone[1] 5,7,4'-trihydroxy-3',5'dimethoxyflavone [2] and 5,7,4'-trihydroxy-3'-methoxyflavone [3] from the whole plant of Viola odorata L and to investigate the antidepressant-like effects of these compounds and their possible mechanism of action using antagonists of the serotonergic, dopaminergic and adrenergic system...
May 15, 2018: Fitoterapia
https://www.readbyqxmd.com/read/29775725/anti-hepatitis-c-virus-activity-and-synergistic-effect-of-nymphaea-alba-extracts-and-bioactive-constituents-in-liver-infected-cells
#14
Sidra Rehman, Usman Ali Ashfaq, Bushra Ijaz, Sheikh Riazuddin
BACKGROUND: Without an effective vaccine, hepatitis C virus (HCV) remains a global threat, inflicting 170-300 million carriers worldwide at risk of cirrhosis and hepatocellular carcinoma (HCC). Though various direct acting antivirals have been redeemed the hepatitis C treatment, a few restraints persist including possible side effects, viral resistance emergence, excessive cost which restricts its availability to a common person. HYPOTHESIS: There is no preventive HCV vaccine available today so the discovery of potent antiviral natural flora and their bioactive constituents may help to develop preventive cures against HCV infection...
May 15, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29774523/acute-and-subacute-antidiabetic-studies-of-enp-9-a-new-1-5-diarylpyrazole-derivative
#15
Eduardo Hernández-Vázquez, Sandra Young-Peralta, Litzia Cerón-Romero, Sara García-Jiménez, Samuel Estrada-Soto
OBJECTIVES: To explore the antihyperglycaemic and antidiabetic effects and to determine the acute toxicity of 5-(4-chlorophenyl)-1-(2,4-dichloro-phenyl)-4-methyl-N-(piperidin-1-yl)-1H-pyrazole-3-carboxamide (ENP-9). METHODS: The antihyperglycaemic effect of ENP-9 (50 mg/kg) was determined by oral glucose tolerance test (OGTT). Also, the acute (16, 50 and 160 mg/kg) and subacute (50 mg/kg/day for 10 days) antidiabetic effects of ENP-9 were determined. After subacute treatment, blood samples were analysed to determine glucose and lipid profiles...
May 17, 2018: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/29773067/in-silico-molecular-docking-and-adme-studies-of-1-3-4-thiadiazole-derivatives-in-relation-to-in-vitro-pon1-activity
#16
Belgin Sever, Kaan Kucukoglu, Hayrunnisa Nadaroglu, Mehlika Dilek Altintop
BACKGROUND: Paraoxonase 1 (PON1) is a paraoxonase, arylesterase and lactonase associated with protection of lipoproteins and cell membranes against oxidative modification. OBJECTIVE: Based on antioxidative properties of PON1 and widely usage of 1,3,4-thiadiazole derivatives in pharmaceutical, agricultural, and materials chemistry, herein we aimed to evaluate PON1 activator potentials of 1,3,4-thiadiazole based compounds. METHOD: 2-[[5-(2,4-Difluoro/dichlorophenylamino)-1,3,4-thiadiazol-2-yl]thio] acetophenone derivatives (1-18), previously synthesized by our research group, were in vitro evaluated for their activator effects on PON1 which was purified using ammonium sulfate precipitation (60-80%) and DEAE-Sephadex anion exchange chromatography...
May 17, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29772746/design-synthesis-and-biological-evaluation-of-benzimidazole-derived-biocompatible-copper-ii-and-zinc-ii-complexes-as-anticancer-chemotherapeutics
#17
Mohamed F AlAjmi, Afzal Hussain, Md Tabish Rehman, Azmat Ali Khan, Perwez Alam Shaikh, Rais Ahmad Khan
Herein, we have synthesized and characterized a new benzimidazole-derived "BnI" ligand and its copper(II) complex, [Cu(BnI)₂], 1 , and zinc(II) complex, [Zn(BnI)₂], 2 , using elemental analysis and various spectroscopic techniques. Interaction of complexes 1 and 2 with the biomolecules viz. HSA (human serum albumin) and DNA were studied using absorption titration, fluorescence techniques, and in silico molecular docking studies. The results exhibited the significant binding propensity of both complexes 1 and 2 , but complex 1 showed more avid binding to HSA and DNA...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29772470/synthesis-molecular-docking-and-xanthine-oxidase-inhibitory-activity-of-5-aryl-1h-tetrazoles
#18
Itrat Fatima, Humaira Zafar, Khalid Mohammed Khan, Syed Muhammad Saad, Sumaira Javaid, Shahnaz Perveen, M Iqbal Choudhary
5-Aryl-1H-tetrazoles (1-24) were synthesized and screened for their xanthine oxidase (XO) inhibitory activity using allopurinol as standard inhibitor (IC50  = 2.0 ± 0.01 µM). Six compounds 3, 4, 5, 9, 21, and 24 exhibited significant to weak activities with IC50 values in the range of 7.4-174.2 µM. Active compounds were further subjected to kinetic and molecular docking studies to deduce their modes of inhibition, and to study their interactions with the protein (XO) at atomic level, respectively...
May 1, 2018: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29772469/synthesis-of-steroidal-imidazolidinthiones-as-potential-apoptotic-agents-investigation-by-theoretical-and-experimental-studies
#19
Ayaz Mahmood Dar, Rizwan Nabi, Shafia Mir, Manzoor Ahmad Gatoo, Shamsuzzaman, Shabir H Lone
New steroidal imidazolidinthione derivatives (4-6) were synthesized from steroidal thiosemicarbazones and dichloroethane. The synthesized compounds were characterized using spectral data analysis. Theoretical DFT involving B3LYP/6-31G∗∗ level of theory was employed to gain insights into the molecular structure of the target compounds. MEPS and FMO analysis were carried out. HOMO-LUMO energy gap was determined which helped to evaluate various global descriptors like hardness, chemical potential, electronegativity, nucleophilicity and electrophilicity index, etc...
May 2, 2018: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29772410/estrogenic-properties-of-coumarins-and-meroterpene-from-the-fruits-of-cullen-corylifolium-experimental-and-computational-studies
#20
Tiehua Zhang, Shuning Zhong, Ligang Hou, Tiezhu Li, XiaoJia Xing, Tianzhu Guan, Jie Zhang, Yongjun Wang
Coumarins and meroterpene from the fruits of Cullen corylifolium were evaluated for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro studies and molecular dynamics simulations. The recombinant hERα ligand binding domain (hERα-LBD) was produced in BL21 (DE3)pLysS and the fluorescence polarization (FP) assay was performed to determine the binding affinities of coumarins and meroterpene with receptor protein. These compounds displayed distinct binding potency toward hERα-LBD, generally increased with their increasing molecular length and Connolly solvent-excluded volume (CSEV)...
May 14, 2018: Phytochemistry
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