keyword
MENU ▼
Read by QxMD icon Read
search

Molecular docking

keyword
https://www.readbyqxmd.com/read/29139502/development-of-the-first-model-of-a-phosphorylated-atp-mg-2-containing-b-raf-monomer-by-molecular-dynamics-simulations-a-tool-for-structure-based-design
#1
Viola Previtali, Cristina Trujillo, Jean-Charles Boisson, Hassan Khartabil, Eric Hénon, Isabel Rozas
A model of phosphorylated and ATP-containing B-Raf protein kinase is needed as a tool for the structure-based design of new allosteric inhibitors, since no crystal structure of such a system has been resolved. Here, we present the development of such a model as well as a thorough analysis of its structural features. This model was prepared using a systematic molecular dynamics approach considering the presence or absence of both the phosphate group at the Thr599 site and the ATP molecule. Then, different structural features (i...
November 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29138965/molecular-dynamics-and-integrated-pharmacophore-based-identification-of-dual-formula-see-text-inhibitors
#2
Maninder Kaur, Pankaj Kumar Singh, Manjinder Singh, Renu Bahadur, Om Silakari
Despite increase in the understanding of the pathogenesis of rheumatoid arthritis (RA), it remains a tough challenge. The advent of kinases involved in key intracellular pathways in pathogenesis of RA may provide a new phase of drug discovery for RA. The present study is aimed to identify dual JAK3/[Formula: see text] inhibitors by developing an optimum pharmacophore model integrating the information revealed by ligand-based pharmacophore models and structure-based pharmacophore models (SBPMs). For JAK3 inhibitors, the addition of an aromatic ring feature and for [Formula: see text] the addition of a hydrophobic feature proposed by SBPMs lead to five-point pharmacophore (i...
November 14, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/29138954/identification-of-compounds-from-palicourea-rigida-leaves-with-topical-anti-inflammatory-potential-using-experimental-models
#3
Rafael P Pinheiro, Muiara A Moraes, Bruna C S Santos, Rodrigo L Fabri, Glauciemar Del-Vechio-Vieira, Célia H Yamamoto, Ana Lúcia S M Araújo, Aílson L A Araújo, Orlando V Sousa
Palicourea rigida Kunth is traditionally used for the treatment of skin diseases, kidney pains and ovarian inflammation. Based on these traditional uses, this study evaluated the topical anti-inflammatory activity of the ethanol extract from P. rigida leaves (EEPR) and identified bioactive compounds. Ear edema was induced in Swiss mice by the topical application of Croton oil, arachidonic acid, phenol and capsaicin. Histopathological analysis and myeloperoxidase and N-acetyl-β-D-glucosaminidase activities were determined...
November 14, 2017: Inflammopharmacology
https://www.readbyqxmd.com/read/29138944/design-synthesis-conformational-and-molecular-docking-study-of-some-novel-acyl-hydrazone-based-molecular-hybrids-as-antimalarial-and-antimicrobial-agents
#4
Parvin Kumar, Kulbir Kadyan, Meenakshi Duhan, Jayant Sindhu, Vineeta Singh, Baljeet Singh Saharan
BACKGROUND: Acyl hydrazones are an important class of heterocyclic compounds promising pharmacological characteristics. Malaria is a life-threatening mosquito-borne blood disease caused by a plasmodium parasite. In some places, malaria can be treated and controlled with early diagnosis. However, some countries lack the resources to do this effectively. RESULTS: The present work involves the design and synthesis of some novel acyl hydrazone based molecular hybrids of 1,4-dihydropyridine and pyrazole (5a-g)...
November 14, 2017: Chemistry Central Journal
https://www.readbyqxmd.com/read/29138774/exploring-the-effect-of-substituent-in-the-hydrazone-ligand-of-a-family-of-%C3%AE-oxidodivanadium-v-hydrazone-complexes-on-structure-dna-binding-and-anticancer-activity
#5
Debashis Patra, Subhabrata Paul, Indira Majumder, Nayim Sepay, Sachinath Bera, Rita Kundu, Michael G B Drew, Tapas Ghosh
The reaction of 2-hydroxybenzoylhydrazine (H2bh) separately with equimolar amounts of [V(IV)O(aa)2] and [V(IV)O(ba)2] in CHCl3 afforded the complexes [VO3(HL(1))2] (1) and [VO3(HL(2))2] (2) respectively in good to excellent yield ((HL(1))(2-) and (HL(2))(2-) represent respectively the dianionic form of 2-hydroxybenzoylhydrazones of acetylacetone (H3L(1)) and benzoylacetone (H3L(2)) (general abbreviation H3L)). From X-ray structure analysis, the V(V)-O-V(V) angle was found to be ∼115° and 180° in 1 and 2 respectively...
November 15, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29138445/inhibition-activity-of-a-traditional-chinese-herbal-formula-huang-lian-jie-du-tang-and-its-major-components-found-in-its-plasma-profile-on-neuraminidase-1
#6
Xuelin Zhou, Haotian Li, Zhilong Shi, Sijia Gao, Shizhang Wei, Kun Li, Jiabo Wang, Jianyu Li, Ruilin Wang, Man Gong, Yanling Zhao, Xiaohe Xiao
Huang-Lian-Jie-Du-Tang (HLJDT), a traditional formula with four TCM herbs, has been used for hundred years for different diseases. The current study aimed to assess the inhibitory activity of HLJDT against H1N1 neuraminidase (NA-1), and identify potent NA-1 inhibitors from its plasma profile. The in vitro NA-1 study has shown that the water extract of HLJDT potently inhibited NA-1 (IC50 = 112.6 μg/ml; Ki = 55.6 μg/ml) in a competitive mode. The IC50 values of the water extracts of its four herbs were as follows: Coptidis Rhizoma, 96...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138424/structure-function-relationships-in-abcg2-insights-from-molecular-dynamics-simulations-and-molecular-docking-studies
#7
Ricardo J Ferreira, Cátia A Bonito, M Natália D S Cordeiro, Maria-José U Ferreira, Daniel J V A Dos Santos
Efflux pumps of the ATP-binding cassette transporters superfamily (ABC transporters) are frequently involved in the multidrug-resistance (MDR) phenomenon in cancer cells. Herein, we describe a new atomistic model for the MDR-related ABCG2 efflux pump, also named breast cancer resistance protein (BCRP), based on the recently published crystallographic structure of the ABCG5/G8 heterodimer sterol transporter, a member of the ABCG family involved in cholesterol homeostasis. By means of molecular dynamics simulations and molecular docking, a far-reaching characterization of the ABCG2 homodimer was obtained...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138086/eugenol-derivatives-prospectively-inhibit-l-asparaginase-a-heady-target-protein-of%C3%A2-salmonella-typhimurium
#8
Archana Vimal, Anubhuti Jha, Awanish Kumar
Salmonella typhimurium is the causative agent of severe human infections and mortality throughout the world. Pacing advent of new resistance mechanisms in this microorganism exists, rendering treatment of infectious disease difficult. Ciprofloxacin is no longer considered the first choice of antimicrobial agent due to the emergence of resistance. Therefore, the need for scenario is to find out novel drug target and its potential inhibitor to fight against this pathogen. The present study was undertaken to find out a novel drug target and its inhibitor for improving the current therapeutic methods for treating Salmonella infections...
November 11, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29137864/synthesis-molecular-docking-and-qsar-study-of-sulfonamide-based-indoles-as-aromatase-inhibitors
#9
Ratchanok Pingaew, Prasit Mandi, Veda Prachayasittikul, Supaluk Prachayasittikul, Somsak Ruchirawat, Virapong Prachayasittikul
Thirty four of indoles bearing sulfonamides (11-44) were synthesized and evaluated for their anti-aromatase activities. Interestingly, all indole derivatives inhibited the aromatase with IC50 range of 0.7-15.3 μM. Indoles (27-36) exerted higher aromatase inhibitory activity than that of ketoconazole. The phenoxy analogs 28 and 34 with methoxy group were shown to be the most potent compounds with sub-micromolar IC50 values (i.e., 0.7 and 0.8 μM, respectively) without affecting to the normal cell line. Molecular docking demonstrated that the indoles 28, 30 and 34 could occupy the same binding site on the aromatase pocket and share several binding residues with those of the natural substrate (androstenedione), which suggested the competitive binding could be the mode of inhibition of the compounds...
October 20, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29137330/virtual-screening-approach-to-identifying-influenza-virus-neuraminidase-inhibitors-using-molecular-docking-combined-with-machine-learning-based-scoring-function
#10
Li Zhang, Hai-Xin Ai, Shi-Meng Li, Meng-Yuan Qi, Jian Zhao, Qi Zhao, Hong-Sheng Liu
In recent years, an epidemic of the highly pathogenic avian influenza H7N9 virus has persisted in China, with a high mortality rate. To develop novel anti-influenza therapies, we have constructed a machine-learning-based scoring function (RF-NA-Score) for the effective virtual screening of lead compounds targeting the viral neuraminidase (NA) protein. RF-NA-Score is more accurate than RF-Score, with a root-mean-square error of 1.46, Pearson's correlation coefficient of 0.707, and Spearman's rank correlation coefficient of 0...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136820/fluorescent-ligand-fishing-combination-with-in-situ-imaging-and-characterizing-to-screen-hsp-90-inhibitors-from-curcuma-longa-l-based-on-inp-zns-quantum-dots-embedded-mesoporous-nanoparticles
#11
Yue Hu, Anchen Fu, Zhaoyi Miao, Xiaojing Zhang, Tianlin Wang, An Kang, Jinjun Shan, Dong Zhu, Wei Li
Although ligand fishing has been shown to be an efficient technique for the identification of bioactive components from complex mixtures such as natural products, it cannot be applied to biomedical image processing. Herein, a specific fluorescent ligand fishing combined with in situ imaging approach is presented for the identification of heat shock protein 90 (Hsp 90) inhibitors from complex matrixes, Curcuma longa L., using N-terminus immobilized Hsp 90α functionalized InP/ZnS quantum dots embedded mesoporous nanoparticles (i...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136775/high-parathyroid-hormone-concentration-in-tenofovir-treated-patients-are-due-to-inhibition-of-calcium-sensing-receptor-activity
#12
Alessandra Mingione, Katia Maruca, Federica Chiappori, Francesca Pivari, Caterina Brasacchio, Tiziana Quirino, Ivan Merelli, Laura Soldati, Paolo Bonfanti, Stefano Mora
Bone health impairment is a common finding in HIV-infected patients on antiretroviral treatment. High serum parathyroid hormone (PTH) concentration in patients on antiretroviral treatment containing tenofovir disoproxil fumarate (TDF) has been reported. Hyperparathyroidism was not always sustained by a reduction in vitamin D concentration. We thus hypothesized a direct inhibitory effect of TDF on the Calcium-sensing receptor (CaSR), leading to hyperparathyroidism. Human embryonic kidney cells were transfected with CASR wild-type gene or mutated in different sites (N124K, T1051G, C788T, T888M)...
November 7, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29136547/natural-products-used-as-a-chemical-library-for-protein-protein-interaction-targeted-drug-discovery
#13
Xuemei Jin, Kyungro Lee, Nam Hee Kim, Hyun Sil Kim, Jong In Yook, Jiwon Choi, Kyoung Tai No
Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery...
October 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29136249/natural-polyphenol-chlorogenic-acid-protects-against-acetaminophen-induced-hepatotoxicity-by-activating-erk-nrf2-antioxidative-pathway
#14
Mengjuan Wei, Zhiyong Zheng, Liang Shi, Yao Jin, Lili Ji
Hepatotoxicity due to acetaminophen (APAP) overdose is a leading cause of drug-induced acute liver failure in clinic. Chlorogenic acid (CGA), a dietary polyphenol, was reported to prevent APAP-induced liver injury in our previous studies. This study aims to investigate the protection provided by CGA against APAP-induced hepatotoxicity via focusing on nuclear factor erythroid 2-related factor 2 (Nrf2) and extracellular regulated protein kinases (ERK)1/2. CGA prevented APAP-induced oxidative liver injury and enhanced Nrf2 activation in mice and in hepatocytes in vitro...
November 10, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29135958/novel-%C3%AE-%C3%AE-unsaturated-sophoridinic-derivatives-design-synthesis-molecular-docking-and-anti-cancer-activities
#15
Yiming Xu, Lichuan Wu, Hang Dai, Mingyan Gao, Haroon Ur Rashid, Haodong Wang, Peng Xie, Xu Liu, Jun Jiang, Lisheng Wang
Using sophoridine 1 and chalcone 3 as the lead compounds, a series of novel α, β-unsaturated sophoridinic derivatives were designed, synthesized, and evaluated for their in vitro cytotoxicity. Structure-activity relationship (SAR) analysis indicated that introduction of α, β-unsaturated ketone moiety and heterocyclic group might significantly enhance anticancer activity. Among the compounds, 2f and 2m exhibited potential effects against HepG-2 and CNE-2 human cancer cell lines. Furthermore, molecular docking studies were performed to understand possible docking sites of the molecules on the target proteins and the mode of binding...
November 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29135926/proline-based-carbamates-as-cholinesterase-inhibitors
#16
Hana Pizova, Marketa Havelkova, Sarka Stepankova, Andrzej Bak, Tereza Kauerova, Violetta Kozik, Michal Oravec, Ales Imramovsky, Peter Kollar, Pavel Bobal, Josef Jampilek
Series of twenty-five benzyl (2S)-2-(arylcarbamoyl)pyrrolidine-1-carboxylates was prepared and completely characterized. All the compounds were tested for their in vitro ability to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), and the selectivity of compounds to individual cholinesterases was determined. Screening of the cytotoxicity of all the compounds was performed using a human monocytic leukaemia THP-1 cell line, and the compounds demonstrated insignificant toxicity. All the compounds showed rather moderate inhibitory effect against AChE; benzyl (2S)-2-[(2-chlorophenyl)carbamoyl]pyrrolidine-1-carboxylate (IC50 = 46...
November 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29135287/molecular-modelling-studies-in-explaining-the-higher-gpvi-antagonistic-activity-of-the-racemic-2-4-methoxyphenylsulfonyl-2-3-4-9-tetrahydro-1h-pyrido-3-4-b-indole-3-carboxamide-than-its-enantiomers
#17
S S Bhunia, A K Saxena
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25...
November 14, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29134430/modern-drug-design-the-implication-of-using-artificial-neuronal-networks-and-multiple-molecular-dynamic-simulations
#18
Oleksandr Yakovenko, Steven J M Jones
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org/ ). The challenge was focused on the ligands of the farnesoid X receptor (FXR), a highly flexible nuclear receptor of the cholesterol derivative chenodeoxycholic acid. FXR is considered an important therapeutic target for metabolic, inflammatory, bowel and obesity related diseases (Expert Opin Drug Metab Toxicol 4:523-532, 2015), but in the context of this competition it is also interesting due to the significant ligand-induced conformational changes displayed by the protein...
November 13, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29133810/selectivity-and-ligand-based-molecular-modeling-of-an-odorant-binding-protein-from-the-leaf-beetle-ambrostoma-quadriimpressum-coleoptera-chrysomelidae-in-relation-to-habitat-related-volatiles
#19
Yinliang Wang, Yincan Jin, Qi Chen, Ming Wen, Hanbo Zhao, Hongxia Duan, Bingzhong Ren
In this study, the most abundant and antenna-specific odorant-binding protein (OBP) of the elm pest A. quadriimpressum, AquaOBP4, was expressed and purified. The selectivity of AquaOBP4 was investigated by screening against a panel of 40 habitat-relevant compounds. Based on the obtained results, a homologous model of AquaOBP4 was established. This model indicated that AquaOBP4 is highly homologous to DmelOBP LUSH and includes two main binding sites. A docking analysis showed that four of five active ligands bound at Site 1, whereas the other ligand was situated at Site 2...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133055/green-unexpected-synthesis-of-bis-coumarin-derivatives-as-potent-anti-bacterial-and-anti-inflammatory-agents
#20
Bahubali M Chougala, S Samundeeswari, Megharaja Holiyachi, Nirmala S Naik, Lokesh A Shastri, Suneel Dodamani, Sunil Jalalpure, Sheshagiri R Dixit, Shrinivas D Joshi, Vinay A Sunagar
A green and efficient protocol has been developed and a series of coumarin based pyrano[3,2-c]chromene derivatives (2) have been synthesized using multi-component reaction (MCR) approach. Unexpected 3-coumarinyl-3-pyrazolylpropanoic acids (3) and C4-C4 chromenes (5) have been isolated instead of expected product 4 by the reaction of compound (2) in formic acid at 90 °C for about 4-5 h and at 130 °C for about 8-10 h respectively. Further, C4-C4chromenes (5) formation was confirmed by intramolecular cyclization of compounds (3)...
October 28, 2017: European Journal of Medicinal Chemistry
keyword
keyword
42951
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"