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Molecular docking

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https://www.readbyqxmd.com/read/28931053/identification-and-molecular-characterization-of-a-metagenome-derived-l-lysine-decarboxylase-gene-from-subtropical-soil-microorganisms
#1
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/28930583/ibuprofen-as-a-template-molecule-for-drug-design-against-ebola-virus
#2
Slobodan Paessler, Cheng Huang, Milan Sencanski, Nevena Veljkovic, Vladimir Perovic, Sanja Glisic, Veljjko Veljkovic
The Ebola virus outbreak in West Africa 2015 and Congo 2017, point out an urgent need for development of drugs against this important pathogen. Previously, by repurposing virtual screening of 6438 drugs from DrugBank, ibuprofen was selected as a possible inhibitor of the Ebola virus infection. The results of an additional docking analysis as well as experimental results showing measurable anti-Ebola effect of ibuprofen in cell culture suggest ibuprofen as a promising molecular template for the development of drugs for treatment of the infection by Ebola virus...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930578/identification-of-bioactive-glucose-lowering-compounds-of-methanolic-extract-of-hodgsonia-heteroclita-fruit-pulp
#3
Talambedu Usha, Arvind Kumar Goyal, Derhasat Narzary, Lokesh Prakash, Gulshan Wadhwa, Dinesh Babu, Divya Shanmugarajan, Sushil Kumar Middha
We have investigated the anti-oxidative and glucose-lowering effects of 70% methanolic extract of H. heteroclita fruit pulp (MHE). Anti-oxidative property of MHE was assessed by free radical scavenging assays and compound level screening by LC-MS profiling. In silico analysis and in vivo preclinical validation were also performed using molecular docking and alloxan-induced diabetic model, respectively. MHE showed high anti-oxidant activity in DPPH radical scavenging assay with an IC50 of 0.37 μg/mL. The LC-MS profile of MHE substantiated the presence of p-hydroxy acids including benzoic, salicylic, p-coumaric, o-coumaric, caffeic, protocatechuic, gentisic, 2,4-dihydroxybenzoic, gallic, vanillic, syringic, and ferulic acids...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28929756/fragment-based-discovery-and-optimization-of-enzyme-inhibitors-by-docking-of-commercial-chemical-space
#4
Axel Rudling, Robert Gustafsson, Ingrid Almlöf, Evert J Homan, Martin Scobie, Ulrika Warpman Berglund, Thomas Helleday, Pål Stenmark, Jens Carlsson
Fragment-based lead discovery has emerged as a leading drug development strategy for novel therapeutic targets. Despite that fragment-based drug discovery benefits immensely from access to atomic-resolution information, structure-based virtual screening has rarely been used to drive fragment discovery and optimization. Here, molecular docking of 0.3 million fragments to a crystal structure of cancer target MTH1 was performed. Twenty-two predicted fragment ligands, for which analogs could be acquired commercially, were experimentally evaluated...
September 20, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28929682/-virtual-screening-for-components-in-chicory-combined-with-cnt2-target-based-on-molecular-docking
#5
Yue Zhou, Bing Zhang, Zhi-Jian Lin, Xiao-Meng Zhang, Fan Li, Hai-Ge Wang, Xue-Jie Wang
To virtual screen the compound of Chicory combined with the concentrative nucleoside transporter 2 (CNT2) in molecular docking technology.The homology model of hCNT2 was produced, and then the Vina software was employed to virtual screen the Chicory compound combined with CNT2. Compared with 7,8,3'-trihydroxyflavone, a CNT2 inhibitors, 23 score higher chicory compounds were hit.Meanwhile, the ten top compounds have been revealed that play important role in decrease the uric level. The bioactivity to CNT2 needs to be investigatedin experiment...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929588/bioactive-compounds-of-shuang-huang-lian-prescription-and-an-insight-into-its-binding-mechanism-by-%C3%AE-2-adrenoceptor-chromatography-coupled-with-site-directed-molecular-docking
#6
Jing Wang, Fengwu Li, Kaizhu Zeng, Qian Li, Xinfeng Zhao, Xiaohui Zheng
Owing to the promising clinical efficacy and relatively simple composition, Shuang-Huang-Lian prescription is widely prescribed for the treatment of acute upper respiratory tract infection and acute bronchitis in practice. This necessitates the understanding of the bioactive compounds of the prescription and their binding mechanism to β2-adrenoceptor, which mediates the aforementioned ailments. In this work, a column containing immobilized β2-adrenoceptor was prepared using a diazonium salt reaction. The bioactive compound collected from the β2-adrenoceptor column was identified as chlorogenic acid by using high-performance liquid chromatography coupled with ion trap mass spectrometry...
September 20, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28929019/heterologous-expression-of-plasmodium-vivax-apical-membrane-antigen-1-pvama1-for-binding-peptide-selection
#7
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/28928721/onion-peel-ethylacetate-fraction-and-its-derived-constituent-quercetin-4-o-%C3%AE-d-glucopyranoside-attenuates-quorum-sensing-regulated-virulence-and-biofilm-formation
#8
Hanan M Al-Yousef, Atallah F Ahmed, Nasser A Al-Shabib, Sameen Laeeq, Rais A Khan, Md T Rehman, Ali Alsalme, Mohamed F Al-Ajmi, Mohammad S Khan, Fohad M Husain
The resistance and pathogenesis of bacteria could be related to their ability to sense and respond to population density, termed quorum sensing (QS). Inhibition of the QS system is considered as a novel strategy for the development of antipathogenic agents, especially for combating drug-resistant bacterial infections. In the present study, the anti-QS activity of Onion peel ethylacetate fraction (ONE) was tested against Chromobacterium violaceum CV12472 and Pseudomonas aeruginosa PAO1. ONE inhibit the QS-mediated virulence factors production such as violacein in C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28927905/synthesis-pharmacological-activities-and-molecular-docking-studies-of-pyrazolyltriazoles-as-anti-bacterial-and-anti-inflammatory-agents
#9
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/28926784/synthesis-of-thiobarbituric-acid-derivatives-in-vitro-%C3%AE-glucosidase-inhibition-and-molecular-docking-studies
#10
Assem Barakat, M Ali, Abdullah Mohammed Al-Majid, Sammer Yousuf, M Iqbal Choudhary, Ruqaiya Khalil, Zaheer Ul-Haq
Synthesis, structure, and evaluation of in vitro α-glucosidase enzyme inhibition of a new class of diethylammonium salts of aryl substituted thiobarbituric acid is described. This protocol is straight, environmentally benign and efficient, involving Aldol-Michael addition reaction in one pot fashion. The 3D chemical structures of the synthesized compounds were assigned based on spectroscopic methods and X-ray single crystal diffraction analyses. All synthesized compounds 3a-3n were evaluated for their in vitro α-glucosidase enzyme inhibitory activity, whereas acarbose was used as the standard drug (IC50=840±1...
September 12, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28926783/molecular-docking-and-qsar-analyses-of-aromatic-heterocycle-thiosemicarbazone-analogues-for-finding-novel-tyrosinase-inhibitors
#11
Huanhuan Dong, Jing Liu, Xiaoru Liu, Yanying Yu, Shuwen Cao
A collection of 36 thiosemicarbazone analogues possessed a broad span of tyrosinase inhibitory activities was designed and obtained. Robust and reliable CoMFA and CoMSIA models were gained to predict the structure-activity relationship and the new modifier direction. Inhibitory activities of the compounds were found to greatly depend upon molecular shape, size, and charge. The sterically bulky group at the C-4 position of the thiophene ring contributed a high capacity for biological activity. Some bulky substituents at the C1-position and C12-position, and electron-negative groups at the C3-position, helped to improve the activity of these analogues...
July 29, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28923390/tnf-%C3%AE-and-il-6-inhibitors-conjugates-of-n-substituted-indole-and-aminophenylmorpholin-3-one-as-anti-inflammatory-agents
#12
Palwinder Singh, Sukhmeet Kaur, Anuradha Sharma, Gurcharan Kaur, Rajbir Bhatti
The conjugates obtained by the combination of indole and aminophenyl morpholinone were screened for TNF-α and IL-6 inhibition in microglial cells. Compound 4 was found to be the most potent anti-inflammatory agent as it reduced LPS induced level of inflammatory cytokines TNF-α and IL-6 by 71% and 53%, respectively. A significant decrease in NO and MMPs release from BV2 cells in culture pretreated with this compound as well as inhibition of nuclear translocation of NF-κB and AP-1 was observed. 75% inhibition of acetic acid induced algesia in swiss albino mice was noticed in the presence of compound 4...
September 4, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28923384/synthesis-and-structure-elucidation-of-novel-salophen-based-dioxo-uranium-vi-complexes-in-vitro-and-in-silico-studies-of-their-dna-bsa-binding-properties-and-anticancer-activity
#13
S Yousef Ebrahimipour, Maryam Mohamadi, Masoud Torkzadeh Mahani, Jim Simpson, Joel T Mague, Iran Sheikhshoaei
The synthesis and characterization of three dioxo U(VI) complexes, [UO2(L(1))(OH2)], [UO2(L(2))DMF], and [UO2(L(2))DMSO], [L(1)](2-) = 1,1'-(4-methyl-1,2-phenylenebis (nitrilomethylidyne))di-2-naphtholate: [L(2)](2-) = 1,1'-(o-phenylenebis (nitrilomethylidyne)) di-2-naphtholate, are reported. Elemental analysis, FT-IR, (1)HNMR, UV-Vis spectroscopy, molar conductivity and single crystal X-ray diffraction were used to characterize the complexes. It was found that the complexes adopt a distorted pentagonal bipyramidal coordination geometry...
September 4, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28923383/design-synthesis-and-structure-activity-relationship-studies-of-a-focused-library-of-pyrimidine-moiety-with-anti-proliferative-and-anti-metastasis-activities-in-triple-negative-breast-cancer
#14
Dahong Yao, Yuxin Zhou, Lingjuan Zhu, Liang Ouyang, Jin Zhang, Yingnan Jiang, Yuqian Zhao, Dejuan Sun, Shilin Yang, Yang Yu, Jinhui Wang
Triple-negative breast cancer (TNBC) is a clinical conundrum with distinct clinical and pathologic features, which is characterized by high aggression, poor prognosis, and lack of targeted therapies. In this study, based on the structural features of type II kinase inhibitors, we designed and synthesized a focused library of 41 pyrimidine derivatives possessing potent anti-proliferation activity, Y29 showed the most potent activity against MDA-MB-231 cells. Subsequently, we carried out target prediction, homology modeling, molecular docking, dynamics simulation and determination of enzymatic activity...
September 15, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28923381/synthesis-of-substituted-phenanthrene-9-benzimidazole-conjugates-cytotoxicity-evaluation-and-apoptosis-inducing-studies
#15
Niggula Praveen Kumar, Pankaj Sharma, S Sujana Kumari, Umarani Brahma, Shalini Nekkanti, Nagula Shankaraiah, Ahmed Kamal
A series of new phenanthrene-9-benzimidazole conjugates has been synthesized by condensing phenanthrene aldehydes with various substituted o-phenylenediamines. The title compounds were evaluated for their in vitro cytotoxic potential against various human cancer cell lines like breast (BT-549), prostate (PC-3 and DU145), triple negative breast cancer (MDA-MB-453), and human colon cancer (HCT-116 and HCT-15) cells. Among the tested compounds, 10o displayed significant in vitro cytotoxic activity against PC-3 prostate cancer cells with an IC50 value of 6...
September 8, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28922971/spectroscopic-and-molecular-docking-studies-on-the-interaction-of-pd-ii-co-ii-schiff-base-complexes-with-%C3%AE-lactoglobulin-as-a-carrier-protein
#16
Monireh Dehkhodaei, Mehdi Sahihi, Hadi Amiri Rudbari
No abstract text is available yet for this article.
September 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28922464/molecular-dynamics-simulation-revealed-binding-of-nucleotide-inhibitors-to-zikv-polymerase-over-444-nanoseconds
#17
Abdo A Elfiky, Wael M Elshemey
In the year 2015, new Zika virus (ZIKV) broke out in Brazil and spread away in more than 80 countries. Scientists directed their efforts toward viral polymerase in attempt to find inhibitors that might interfere with its function. In this study, molecular dynamics simulation (MDS) was performed over 444 ns for a ZIKV polymerase model. Molecular docking (MD) was then performed every 10 ns during the MDS course to ensure the binding of small molecules to the polymerase over the entire time of the simulation...
September 18, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28921381/pentachlorophenol-molecule-design-with-lower-bioconcentration-through-3d-qsar-associated-with-molecule-docking
#18
Xiaolei Wang, Zhenhua Chu, Jiawen Yang, Yu Li
A three-dimensional quantitative structure activity relationship (3D-QSAR) model is built by using a comparative molecular similarity indices analysis (CoMSIA) technique with an experimentally determined logarithm of bioconcentration factors (logBCFs) for 36 phenols in fish. Meanwhile, with the pentachlorophenol (PCP) molecule as target molecules, contributions of the molecular fields indicate that the electrostatic fields are the main influences on the bioconcentration of the PCP molecule. Based on the analytical results of CoMSIA contour map of PCP and PCP molecular docking with SOD protease (PDB ID: 4A7T), the R6 substituent positions of PCP were modified to give seven new modified PCP molecules with low bioconcentration in this paper...
September 18, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28921375/convex-pl-a-novel-knowledge-based-potential-for-protein-ligand-interactions-deduced-from-structural-databases-using-convex-optimization
#19
Maria Kadukova, Sergei Grudinin
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and deduce the expansion coefficients from the structural knowledge base using a convex formulation of the optimization problem. Also, for the training set we do not generate false poses with molecular docking packages, but use constant RMSD rigid-body deformations of the ligands inside the binding pockets...
September 18, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28921079/identification-of-a-new-isoindole-2-yl-scaffold-as-a-qo-and-qi-dual-inhibitor-of-cytochrome-bc-1-complex-virtual-screening-synthesis-and-biochemical-assay
#20
Homa Azizian, Kowsar Bagherzadeh, Sophia Shahbazi, Niusha Sharifi, Massoud Amanlou
Respiratory chain ubiquinol-cytochrome (cyt) c oxidoreductase (cyt bc 1 or complex III) has been demonstrated as a promising target for numerous antibiotics and fungicide applications. In this study, a virtual screening of NCI diversity database was carried out in order to find novel Qo/Qi cyt bc 1 complex inhibitors. Structure-based virtual screening and molecular docking methodology were employed to further screen compounds with inhibition activity against cyt bc 1 complex after extensive reliability validation protocol with cross-docking method and identification of the best score functions...
September 18, 2017: Interdisciplinary Sciences, Computational Life Sciences
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