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Molecular docking

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https://www.readbyqxmd.com/read/28646405/revealing-the-importance-of-linkers-in-k-series-oxime-reactivators-for-tabun-inhibited-ache-using-quantum-chemical-docking-and-smd-studies
#1
Shibaji Ghosh, Nellore Bhanu Chandar, Kalyanashis Jana, Bishwajit Ganguly
Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators for tabun-inhibited AChE than (K027, K127, and K628). These reactivators differ only in the linker units between the two pyridinium rings. The conformational analyses performed with quantum chemical RHF/6-31G* level for K027, K127, K203 and K628 showed that the minimum energy conformers have different orientations of the active and peripheral pyridinium rings for these reactivator molecules...
June 23, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28644553/structural-insights-into-the-inclusion-complexes-between-clomiphene-citrate-and-%C3%AE-cyclodextrin-the-mechanism-of-preferential-isomeric-selection
#2
Arti Maheshwari, Harish Saraswat, Santosh Kumar Upadhyay
A major challenge in pharmaceuticals for clinical applications is to alter the solubility, stability, and toxicity of drug molecules in living systems. Cyclodextrins (CDs) have the ability to form host-guest inclusion complexes with pharmaceuticals for further development of new drug formulations. The inclusion complex of clomiphene citrate (CL), a poorly water-soluble drug, with native β-cyclodextrin (β-CD) was characterized by a one and two-dimensional nuclear magnetic resonance (NMR) spectroscopic approach and also by molecular docking techniques...
June 23, 2017: Chirality
https://www.readbyqxmd.com/read/28643389/combined-molecular-modelling-and-3d-qsar-study-for-understanding-the-inhibition-of-nqo1-by-heterocyclic-quinone-derivatives
#3
Claudia Lopez-Lira, Jans H Alzate-Morales, Margot Paulino, Jaime Mella-Raipán, Cristian O Salas, Ricardo A Tapia, Jorge Soto-Delgado
A combination of three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular modelling methods were used to understand the potent inhibitory NAD(P)H:quinone oxidoreductase 1 (NQO1) activity of a set of 52 heterocyclic quinones. Molecular docking results indicated that some favourable interactions of key amino acid residues at the binding site of NQO1 with these quinones, would be responsible for an improvement of the NQO1 activity of these compounds. The main interactions involved are hydrogen bond of the amino group of residue Tyr128, π-stacking interactions with Phe106 and Phe178, and electrostatic interactions with flavin adenine dinucleotide (FADH) cofactor...
June 23, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28642707/tetrandrine-an-activator-of-autophagy-induces-autophagic-cell-death-via-pkc-%C3%AE-inhibition-and-mtor-dependent-mechanisms
#4
Vincent Kam Wai Wong, Wu Zeng, Juan Chen, Xiao Jun Yao, Elaine Lai Han Leung, Qian Qian Wang, Pauline Chiu, Ben C B Ko, Betty Yuen Kwan Law
Emerging evidence suggests the therapeutic role of autophagic modulators in cancer therapy. This study aims to identify novel traditional Chinese medicinal herbs as potential anti-tumor agents through autophagic induction, which finally lead to autophagy mediated-cell death in apoptosis-resistant cancer cells. Using bioactivity-guided purification, we identified tetrandrine (Tet) from herbal plant, Radix stephaniae tetrandrae, as an inducer of autophagy. Across a number of cancer cell lines, we found that breast cancer cells treated with tetrandrine show an increase autophagic flux and formation of autophagosomes...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28641834/establishment-and-molecular-modeling-study-of-maltodextrin-based-synergistic-enantioseparation-systems-with-two-new-hydroxy-acid-chiral-ionic-liquids-as-additives-in-capillary-electrophoresis
#5
Xuan Yang, Yingxiang Du, Zijie Feng, Zongran Liu, Jingtang Li
Discovering more superior performance of ionic liquids for the separation science has triggered increasing interest. In this work, two new Hydroxy acid-based chiral ionic liquids (CILs) (tertramethylammonium-d-pantothenate (TMA-d-PAN), tertramethylammonium-d-quinate (TMA-d-QUI)) were designed and first used as additives to establish the maltodextrin-based synergistic systems for enantioseparation in capillary electrophoresis (CE). Compared to traditional single maltodextrin chiral separation system, significantly improved separations of all tested drugs in the CIL/Maltodextrin synergistic systems were obtained...
June 2, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28641528/drug-design-synthesis-and-in-vitro-evaluation-of-substituted-benzofurans-as-hsp90-inhibitors
#6
Sundeep Kadasi, Thadeu E M M Costa, Neha Arukala, Mallika Toshakani, Chaitanya Duggineti, Sreekanth Thota, Sayan Dutta Gupta, Shiva Raj, Carmen Penido, Maria G Henriques, Nulgumnalli Manjunathaiah Raghavendra
BACKGROUND: Heat shock protein 90 is a molecular chaperone required for the stability and function of several client proteins that promote cancer cell growth and/or survival. Discovery of Hsp90 inhibitors has emerged as an attractive target of research in cancer therapeutics. Natural products like geldanamycin and radicicol are established Hsp90 inhibitors, but face limitations with toxicity and inactivity, by in vivo studies respectively. However, they lay the logical starting point for the design of novel synthetic or semi-synthetic congeners as Hsp90 inhibitors...
June 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28641512/molecular-docking-and-molecular-dynamics-simulation-based-approach-to-explore-the-dual-inhibitor-against-hiv-1-reverse-transcriptase-and-integrase
#7
Subhash Chander, Rajan Kumar Pandey, Ashok Penta, Bhanwar Singh Choudhary, Manish Sharma, Ruchi Malik, Vijay Kumar Prajapati, Sankaranarayanan Murugesan
HIV integrase (IN) and reverse transcriptase (RT) are key enzymes for the replication of HIV-1. DNA polymerase and ribonuclease H (RNase H) are the two catalytic domains of HIV-1 RT which are validated as drug targets because of their essence for replication. IN and RNase H domain of RT share the striking structural similarity; it contains conserved DDE triad (two aspartates and one glutamate) and a pair of divalent Mg2+/Mn2+ ions at their catalytic core domain. Therefore, the search of compounds with dual inhibition of IN and RNase H can be the viable and more efficacious approach for the drug development against both wild and drug resistance strains of HIV...
June 15, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28641189/qualitative-and-quantitative-simulation-of-androgen-receptor-antagonists-a-case-study-of-polybrominated-diphenyl-ethers
#8
Yang Wu, Wei Shi, Pu Xia, Xiaowei Zhang, Hongxia Yu
Recently, great attention has been paid to the identification and prediction of the androgen disrupting potencies of polybrominated diphenyl ethers (PBDEs). However, few existing models can discriminate active and inactive compounds, which make the quantitative prediction process including the quantitative structure-activity relationship (QSAR) technique unreliable. In this study, different grouping methods were investigated and compared for qualitative identification, including molecular docking and molecular dynamics simulations (MD)...
June 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28640852/differential-roles-of-3-hydroxyflavone-and-7-hydroxyflavone-against-nicotine-induced-oxidative-stress-in-rat-renal-proximal-tubule-cells
#9
Bidisha Sengupta, Mehdi Sahihi, Monireh Dehkhodaei, Darrian Kelly, Istvan Arany
Plant flavonoids are well known as antioxidants against oxidative stress induced by exposure to external pollutants. Nicotine (NIC) is one of those agents which increases renal oxidative stress, an important factor in the pathogenesis of renal epithelial injury in smokers. Although several studies had been conducted on flavonoids and oxidative stress, the mechanism of the protective pathways are not fully understood. Here, we present studies on antioxidant properties of two mono-hydroxyflavone isomers, 3-hydroxyflanove (3HF)- and 7-hydroxyflavone (7HF), against nicotine-associated oxidative stress and injury in cultured renal proximal tubule cells and correlate their antioxidant properties with their chemical structure...
2017: PloS One
https://www.readbyqxmd.com/read/28640592/identification-of-a-small-molecule-activator-for-aphb-a-lysr-type-virulence-transcriptional-regulator-in-vibrio-cholerae
#10
Britney Privett, Maria Pellegrini, Gabriela Kovacikova, Ronald Taylor, Karen Skorupski, Dale F Mierke, F Jon Kull
AphB is a LysR-type transcriptional regulator (LTTR) that cooperates with a second transcriptional activator, AphA, at the tcpPH promoter to initiate expression of the virulence cascade in Vibrio cholerae. Since it is not yet known whether AphB responds to a natural ligand in V. cholerae that influences its ability to activate transcription, we used a computational approach to identify small molecules that influence its activity. In silico docking was used to identify potential ligands for AphB, and saturation transfer difference NMR was subsequently employed to access the validity of promising targets...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28640302/influence-of-substituents-on-dna-and-protein-binding-of-cyclometalated-ir-iii-complexes-and-anticancer-activity
#11
Sujay Mukhopadhyay, Roop Shikha Singh, Rajendra Prasad Paitandi, Gunjan Sharma, Biplob Koch, Daya Shankar Pandey
Synthesis of terpyridyl based ligands 3-([2,2':6',2''-terpyridin]-4'-yl)-7-methoxy-2-(methylthio)-quinolone, (L1); 3-([2,2':6',2''-terpyridin]-4'-yl)-6-methoxyquinolin-2(1H)-one, (L2); 3-([2,2'-:6',2''-terpyridin]-4'-yl)-6-methylquinolin-2(1H)-one (L3) and cyclometalated iridium(iii) complexes [[Ir(ppy)2L1](+)PF6(-) (1), [Ir(ppy)2L2](+)PF6(-) (2), [Ir(ppy)2L3](+)PF6(-) (3) (2-phenylpyridine = Hppy)] involving these ligands has been described. The ligands L1-L3 and complexes 1-3 have been thoroughly characterized by elemental analyses, spectral studies (IR, (1)H, (13)C NMR, UV/vis and fluorescence) ESI-MS, and the structure of 3 has been unambiguously authenticated by single crystal X-ray analyses...
June 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28639379/the-in-vitro-and-in-vivo-biological-activities-of-the-leaf-of-cape-myrtle-myrsine-africana-l
#12
Hina Gul, Mushtaq Ahmad, Muhammad Zafar, M Shareez Ahmad, AmbreenAbid, Syeda Hira, Imam Shah, Muhammad Gulfraz
The cape myrtle, Myrsine africana L., is a widely used medicinal plant, which has not been well investigated. We assessed the in vivo hepatoprotective and in vitro antiproliferative and antioxidant effects of leaf extracts of M. africana chemically profiled using high-performance liquid chromatography. Three flavonoids were quantified, and gas chromatography-mass spectrometry analysis revealed the presence of common fatty acids. The animal study was conducted on mice treated with CCl4, using three doses each of the methanol and chloroform extract (100, 200 and 300 mg/kg b...
June 22, 2017: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/28638340/neurologically-potent-molecules-from-crataegus-oxyacantha-isolation-anticholinesterase-inhibition-and-molecular-docking
#13
Mumtaz Ali, Sultan Muhammad, Muhammad R Shah, Ajmal Khan, Umer Rashid, Umar Farooq, Farhat Ullah, Abdul Sadiq, Muhammad Ayaz, Majid Ali, Manzoor Ahmad, Abdul Latif
Crataegus oxyacantha is an important herbal supplement and famous for its antioxidant potential. The antioxidant in combination with anticholinesterase activity can be considered as an important target in the management of Alzheimer's disease. The compounds isolated from C. oxyacantha were evaluated for cholinesterases inhibitory activity using Ellman's assay with Galantamine as standard drug. Total of nine (1-9) compounds were isolated. Compounds 1 and 2 were isolated for the first time from natural source...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28637675/structure-functional-aspects-of-the-human-riboflavin-transporter-3-slc52a3-role-of-the-predicted-glycosylation-and-substrate-interacting-sites
#14
Veedamali S Subramanian, Subrata Subai, Trevor Teafatiller, Jennifer A Bohl, Hamid M Said
The human riboflavin (RF) transporter-3 (hRFVT-3; product of the SLC52A3 gene) plays an essential role in the intestinal RF absorption process and is expressed exclusively at the apical membrane domain of polarized enterocytes. Previous studies have characterized different physiological/biological aspects of this transporter, but nothing is known about the glycosylation status of the hRFVT-3 protein and role of this modification in its physiology/biology. Additionally, little is known about the residues in the hRFVT-3 protein that interact with the ligand, RF...
June 21, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/28637443/trichoderma-virens-%C3%AE-glucosidase-i-bgli-gene-expression-in-saccharomyces-cerevisiae-including-docking-and-molecular-dynamics-studies
#15
Gammadde Hewa Ishan Maduka Wickramasinghe, Pilimathalawe Panditharathna Attanayake Mudiyanselage Samith Indika Rathnayake, Naduviladath Vishvanath Chandrasekharan, Mahindagoda Siril Samantha Weerasinghe, Ravindra Lakshman Chundananda Wijesundera, Wijepurage Sandhya Sulochana Wijesundera
BACKGROUND: Cellulose, a linear polymer of β 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and β-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose. As it is well known, Saccharomyces cerevisiae can efficiently convert glucose into ethanol under anaerobic conditions...
June 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28636281/aryl-and-heteroaryl-substituted-phenylalanines-as-ampa-receptor-ligands
#16
Ewa Szymańska, Paulina Chałupnik, Tommy N Johansen, Birgitte Nielsen, Ana Maria Cuñado Moral, Darryl S Pickering, Anna Więckowska, Katarzyna Kieć-Kononowicz
A series of racemic unnatural amino acids was rationally designed on the basis of recently published X-ray structures of the GluA2 LBD with bound phenylalanine-based antagonists. Twelve new diaryl- or aryl/heteroaryl-substituted phenylalanine derivatives were synthesized and evaluated in vitro in radioligand binding assays at native rat ionotropic glutamate receptors. The most interesting compound in this series, (RS)-2-amino-3-(3'-hydroxy-5-(1H-pyrazol-4-yl)-[1,1'-biphenyl]-3-yl)propanoic acid 7e, showed the binding affinity of 4...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28636189/discovery-of-alkyl-bis-oxy-dibenzimidamide-derivatives-as-novel-protein-arginine-methyltransferase-1-prmt1-inhibitors
#17
Wei-Yao Zhang, Wen-Chao Lu, Hao Jiang, Zheng-Bing Lv, Yi-Qian Xie, Fu-Lin Lian, Zhong-Jie Liang, Yu-Xi Jiang, Da-Jin Wang, Cheng Luo, Jia Jin, Fei Ye
Protein arginine methylation, a post-translational modification critical for a variety of biological processes, is catalyzed by protein arginine N-methyltransferases (PRMTs). In particular, PRMT1 is responsible for over 85% of the arginine methylation in mammalian cells. Dysregulation of PRMT1 is involved in diverse pathological diseases including cancers. However, most current PRMT1inhibitors are lack of specificity, efficacy, and bioavailability. Herein, a series of alkyl bis(oxy)dibenzimidamide derivatives were identified as selective PRMT1 inhibitors...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28635653/virtual-screening-against-phosphoglycerate-kinase-1-in-quest-of-novel-apoptosis-inhibitors
#18
Jie Xia, Bo Feng, Qianhang Shao, Yuhe Yuan, Xiang Simon Wang, Naihong Chen, Song Wu
Inhibition of apoptosis is a potential therapy to treat human diseases such as neurodegenerative disorders (e.g., Parkinson's disease), stroke, and sepsis. Due to the lack of druggable targets, it remains a major challenge to discover apoptosis inhibitors. The recent repositioning of a marketed drug (i.e., terazosin) as an anti-apoptotic agent uncovered a novel target (i.e., human phosphoglycerate kinase 1 (hPgk1)). In this study, we developed a virtual screening (VS) pipeline based on the X-ray structure of Pgk1/terazosin complex and applied it to a screening campaign for potential anti-apoptotic agents...
June 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28635645/cembrene-diterpenoids-with-ether-linkages-from-sarcophyton-ehrenbergi-an-anti-proliferation-and-molecular-docking-assessment
#19
Mohamed-Elamir F Hegazy, Abdelsamed I Elshamy, Tarik A Mohamed, Ahmed R Hamed, Mahmoud A A Ibrahim, Shinji Ohta, Paul W Paré
Three new cembrene diterpenoids, sarcoehrenbergilid A-C (1-3), along with four known diterpenoids, sarcophine (4), (+)-7α,8β-dihydroxydeepoxysarcophine (5), sinulolide A (6), and sinulolide B (7), and one steroid, sardisterol (8), were isolated and characterized from a solvent extract of the Red Sea soft coral Sarcophyton ehrenbergi. Chemical structures were elucidated by NMR and MS analyses with absolute stereochemistry determined by X-ray analysis. Since these isolated cembrene diterpenes contained 10 or more carbons in a large flexible ring, conformer stabilities were examined based on density functional theory calculations...
June 21, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28635308/combined-hqsar-topomer-comfa-homology-modeling-and-docking-studies-on-triazole-derivatives-as-sglt2-inhibitors
#20
Shuling Yu, Jintao Yuan, Yi Zhang, Shufang Gao, Ying Gan, Meng Han, Yuewen Chen, Qiaoqiao Zhou, Jiahua Shi
AIM: Sodium-glucose cotransporter 2 (SGLT2) is a promising target for diabetes therapy. We aimed to develop computational approaches to identify structural features for more potential SGLT2 inhibitors. MATERIALS & METHODS: In this work, 46 triazole derivatives as SGLT2 inhibitors were studied using a combination of several approaches, including hologram quantitative structure-activity relationships (HQSAR), topomer comparative molecular field analysis (CoMFA), homology modeling, and molecular docking...
June 21, 2017: Future Medicinal Chemistry
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