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Molecular docking

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https://www.readbyqxmd.com/read/28214932/theoretical-and-experimental-study-of-polycyclic-aromatic-compounds-as-%C3%AE-tubulin-inhibitors
#1
Fabian E Olazarán, Carlos A García-Pérez, Debasish Bandyopadhyay, Isaias Balderas-Rentería, Angel D Reyes-Figueroa, Lars Henschke, Gildardo Rivera
In this work, through a docking analysis of compounds from the ZINC chemical library on human β-tubulin using high performance computer cluster, we report new polycyclic aromatic compounds that bind with high energy on the colchicine binding site of β-tubulin, suggesting three new key amino acids. However, molecular dynamic analysis showed low stability in the interaction between ligand and receptor. Results were confirmed experimentally in in vitro and in vivo models that suggest that molecular dynamics simulation is the best option to find new potential β-tubulin inhibitors...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28214775/role-of-c-di-gmp-in-anammox-aggregation-and-systematic-analysis-of-its-turnover-protein-in-candidatus-jettenia-caeni
#2
Yongzhao Guo, Sitong Liu, Xi Tang, Fenglin Yang
The anaerobic ammonium oxidation (anammox) process has been recognized as a promising sewage treatment approach. Considering the susceptibility, it is meaningful to study the behaviors of anammox bacteria under the unfavorable conditions. Here, we found that anammox bacteria more probably tended to aggregation by the regulation of c-di-GMP against the unfavorable environmental stresses (low temperature, aerobic condition and low pH). Further using multiple protein sequence alignment, we systematically examined the functionality of thirteen genes encoding putative c-di-GMP metabolic enzymes in anammox organism Candidatus Jettenia caeni, revealing most of the predicted enzymes were predicted to be active...
February 12, 2017: Water Research
https://www.readbyqxmd.com/read/28214753/structural-and-functional-insights-into-corrinoid-iron-sulfur-protein-from-human-pathogen-clostridium-difficile
#3
Yaozhu Wei, Xiaofei Zhu, Sixue Zhang, Xiangshi Tan
The human pathogen Clostridium difficile infection (CDI) is one of the most important healthcare-associated infections. The Wood-Ljungdahl pathway, which is responsible for Acetyl-CoA biosynthesis, is essential for the survival of the pathogen and is absent in humans. The key proteins and enzymes involved in the pathway are attractive targets for the treatment of CDI. Corrinoid iron-sulfur protein (CoFeSP) is a key protein and acts as a methyl transformer in the Wood-Ljungdahl pathway. In this study, CoFeSP from Clostridium difficile (CoFeSPCd) was cloned, expressed in E...
February 13, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28214631/discovery-of-quinone-directed-antitumor-agents-selectively-bioactivated-by-nqo1-over-cpr-with-improved-safety-profile
#4
Jinlei Bian, Xiang Li, Nan Wang, Xingsen Wu, Qidong You, Xiaojin Zhang
In this work, we mainly focused on discovering compounds with good selectivity for NQO1 over CPR. The NQO1-mediated two-electron reduction of compounds would kill cancer cells selectively, while CPR-mediated one-electron reduction would induce potential hepatotoxicity. Several novel quinone-directed antitumor agents were discovered as specific NQO1 substrates through structure-activity relationship studies. Among them, compound 3,7,8-trimethylnaphtho[1,2-b]furan-4,5-dione (12b) emerged as the most specific substrate of the two-electron oxidoreductase NQO1 and could hardly be reduced by CPR...
February 6, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28214077/new-homoisoflavonoid-analogues-protect-cells-by-regulating-autophagy
#5
Li-She Gan, Lin-Wei Zeng, Xiang-Rong Li, Chang-Xin Zhou, Jie Li
As a special group of naturally occurring flavonoids, homoisoflavonoids have been discovered as active components of several traditional Chinese medicines for nourishing heart and mind. In this study, twenty homoisoflavonoid analogues, including different substitution groups on rings A and B, as well as heteroaromatic B ring, were synthesized and evaluated for their cardioprotective and neuroprotective activities. In a H2O2-induced H9c2 cardiomyocytes injury assay, nine homoisoflavonoid analogues showed promising activities in the same level as the positive control, diazoxide...
February 1, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28213174/evidence-of-the-presence-of-a-calmodulin-sensitive-plasma-membrane-ca-2-atpase-in-trypanosoma-equiperdum
#6
María Carolina Pérez-Gordones, José Rubén Ramírez-Iglesias, Vincenza Cervino, Graciela L Uzcanga, Gustavo Benaim, Marta Mendoza
Trypanosoma equiperdum belongs to the subgenus Trypanozoon, which has a significant socio-economic impact by limiting animal protein productivity worldwide. Proteins involved in the intracellular Ca(2+) regulation are prospective chemotherapeutic targets since several drugs used in experimental treatment against trypanosomatids exert their action through the disruption of the parasite intracellular Ca(2+) homeostasis. Therefore, the plasma membrane Ca(2+)-ATPase (PMCA) is considered as a potential drug target...
February 14, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28212383/novel-molecular-structural-and-evolutionary-characteristics-of-the-phosphoketolases-from-bifidobacteria-and-coriobacteriales
#7
Radhey S Gupta, Anish Nanda, Bijendra Khadka
Members from the order Bifidobacteriales, which include many species exhibiting health promoting effects, differ from all other organisms in using a unique pathway for carbohydrate metabolism, known as the "bifid shunt", which utilizes the enzyme phosphoketolase (PK) to carry out the phosphorolysis of both fructose-6-phosphate (F6P) and xylulose-5-phosphate (X5P). In contrast to bifidobacteria, the PKs found in other organisms (referred to XPK) are able to metabolize primarily X5P and show very little activity towards F6P...
2017: PloS One
https://www.readbyqxmd.com/read/28212337/synthesis-anti-breast-cancer-activity-and-molecular-docking-study-of-a-new-group-of-acetylenic-quinolinesulfonamide-derivatives
#8
Krzysztof Marciniec, Bartosz Pawełczak, Małgorzata Latocha, Leszek Skrzypek, Małgorzata Maciążek-Jurczyk, Stanisław Boryczka
In this study, a series of regioisomeric acetylenic sulfamoylquinolines are designed, synthesized, and tested in vitro for their antiproliferative activity against three human breast cacer cell lines (T47D, MCF-7, and MDA-MB-231) and a human normal fibroblast (HFF-1) by 4-[3-(4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio]-1,3-benzene disulfonate (WST-1) assay. The antiproliferative activity of the tested acetylenic quinolinesulfonamides is comparable to that of cisplatin. The bioassay results demonstrate that most of the tested compounds show potent antitumor activities, and that some compounds exhibit better effects than the positive control cisplatin against various cancer cell lines...
February 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28211920/evaluation-of-acridine-orange-derivatives-as-dna-targeted-radiopharmaceuticals-for-auger-therapy-influence-of-the-radionuclide-and-distance-to-dna
#9
Edgar Pereira, Letícia do Quental, Elisa Palma, Maria Cristina Oliveira, Filipa Mendes, Paula Raposinho, Isabel Correia, João Lavrado, Salvatore Di Maria, Ana Belchior, Pedro Vaz, Isabel Santos, António Paulo
A new family of (99m)Tc(I)- tricarbonyl complexes and (125)I-heteroaromatic compounds bearing an acridine orange (AO) DNA targeting unit was evaluated for Auger therapy. Characterization of the DNA interaction, performed with the non-radioactive Re and (127)I congeners, confirmed that all compounds act as DNA intercalators. Both classes of compounds induce double strand breaks (DSB) in plasmid DNA but the extent of DNA damage is strongly dependent on the linker between the Auger emitter ((99m)Tc or (125)I) and the AO moiety...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211616/design-synthesis-and-biological-evaluation-of-chalcone-containing-shikonin-derivatives-as-inhibitors-of-tubulin-polymerization
#10
Han-Yue Qiu, Fang Wang, Xue Wang, Wen-Xue Sun, Jin-Liang Qi, Yan-Jun Pang, Rong-Wu Yang, Gui-Hua Lu, Xiao-Ming Wang, Yong-Hua Yang
The biological importance of microtubules in mitosis makes them an interesting target for the development of anticancer agents. In this study, a series of novel chalcone-containing shikonin derivatives was designed, synthesized, and evaluated for biological activities. Among them, derivative PMMB-259 [(R)-1-(5,8-dihydroxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-4-methylpent-3-en-1-yl (E)-2-(4-(3-oxo-3-(3-(trifluoromethoxy)phenyl)prop-1-en-1-yl)phenoxy)acetate] was identified as a potent inhibitor of tubulin polymerization...
February 17, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28211580/inhibition-of-pde5a1-guanosine-cyclic-monophosphate-cgmp-hydrolysing-activity-by-sildenafil-analogues-that-inhibit-cellular-cgmp-efflux
#11
Anna Subbotina, Aina W Ravna, Roy A Lysaa, Ruben Abagyan, Ryszard Bugno, Georg Sager
OBJECTIVES: To determine the ability of 11 sildenafil analogues to discriminate between cyclic nucleotide phosphodiesterases (cnPDEs) and to characterise their inhibitory potencies (Ki values) of PDE5A1-dependent guanosine cyclic monophosphate (cGMP) hydrolysis. METHODS: Sildenafil analogues were identified by virtual ligand screening (VLS) and screened for their ability to inhibit adenosine cyclic monophosphate (cAMP) hydrolysis by PDE1A1, PDE1B1, PDE2A1, PDE3A, PDE10A1 and PDE10A2, and cGMP hydrolysis by PDE5A, PDE6C, PDE9A2 for a low (1 nm) and high concentration (10 μm)...
February 17, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28210904/acute-and-neuropathic-orofacial-antinociceptive-effect-of-eucalyptol
#12
José de Maria de Albuquerque de Melo Júnior, Marina de Barros Mamede Vidal Damasceno, Sacha Aubrey Alves Rodrigues Santos, Talita Matias Barbosa, João Ronielly Campêlo Araújo, Antonio Eufrásio Vieira-Neto, Deysi Viviana Tenazoa Wong, Roberto César Pereira Lima-Júnior, Adriana Rolim Campos
Terpenes have a wide range of pharmacological properties, including antinociceptive action. The anti-inflammatory and antinociceptive effects of eucalyptol are well established. The purpose of this study was to evaluate the antinociceptive effect of eucalyptol on acute and neuropathic orofacial pain in rodent models. Acute orofacial and corneal nociception was induced with formalin, capsaicin, glutamate and hypertonic saline in mice. In another series, animals were pretreated with capsazepine or ruthenium red to evaluate the involvement of TRPV1 receptors in the effect of eucalyptol...
February 16, 2017: Inflammopharmacology
https://www.readbyqxmd.com/read/28210726/exploring-the-interaction-of-phenothiazinium-dyes-methylene-blue-new-methylene-blue-azure-a-and-azure-b-with-trna-phe-spectroscopic-thermodynamic-voltammetric-and-molecular-modeling-approach
#13
Puja Paul, Soumya Sundar Mati, Subhash Chandra Bhattacharya, Gopinatha Suresh Kumar
This study focuses on the understanding of the interaction of phenothiazinium dyes methylene blue (MB), new methylene blue (NMB), azure A (AZA) and azure B (AZB) with tRNA(Phe) with particular emphasis on deciphering the mode and energetics of the binding. Strong intercalative binding to tRNA(Phe) was observed for MB, NMB and AZB, bound by a partial intercalative mode. AZA has shown groove binding characteristics. From spectroscopic studies binding affinity values of the order of 10(5) M(-1) were deduced for these dyes; the trend varied as MB > NMB > AZB > AZA...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28208727/bioactive-benzofuran-derivatives-from-cortex-mori-radicis-and-their-neuroprotective-and-analgesic-activities-mediated-by-mglur%C3%A2
#14
Ya-Nan Wang, Mao-Feng Liu, Wei-Zhen Hou, Rui-Ming Xu, Jie Gao, An-Qi Lu, Mei-Ping Xie, Lan Li, Jian-Jun Zhang, Ying Peng, Li-Li Ma, Xiao-Liang Wang, Jian-Gong Shi, Su-Juan Wang
Four new benzofuran-type stilbene glycosides and 14 known compounds including 8 benzofuran-type stilbenes and 6 flavonoids were isolated from the traditional Chinese medicine, Cortex Mori Radicis. The new compounds were identified as (9R)-moracin P 3'-O-α-l-arabinopyranoside (1), (9R)-moracin P 9-O-β-d-glucopyranoside (2), (9R)-moracin P 3'-O-β-d-glucopyranoside (3), and (9R)-moracin O 10-O-β-d-glucopyranoside (4) based on the spectroscopic interpretation and chemical analysis. Three benzofuran-type stilbenes, moracin O (5), R (7), and P (8) showed significant neuroprotective activity against glutamate-induced cell death in SK-N-SH cells...
February 8, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28208662/characterization-molecular-docking-and-in-vitro-dissolution-studies-of-solid-dispersions-of-20-s-protopanaxadiol
#15
Qi Zhang, Yiqiong Pu, Bing Wang, Yuqin Wang, Tina Tingxia Dong, Tao Guo, Tong Zhang, Zhenzhen Cai
In this study, we prepared solid dispersions (SDs) of 20(S)-protopanaxadiol (PPD) using a melting-solvent method with different polymers, in order to improve the solubility and dissolution performance of drugs with poor water solubility. The SDs were characterized via differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and molecular docking and dynamics study. DSC and PXRD results indicated that PPD crystallinity in SDs was significantly reduced, and that the majority of PPD is amorphous...
February 11, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28207811/accelerated-flexible-protein-ligand-docking-using-hamiltonian-replica-exchange-with-a-repulsive-biasing-potential
#16
Katja Ostermeir, Martin Zacharias
A molecular dynamics replica exchange based method has been developed that allows rapid identification of putative ligand binding sites on the surface of biomolecules. The approach employs a set of ambiguity restraints in replica simulations between receptor and ligand that allow close contacts in the reference replica but promotes transient dissociation in higher replicas. This avoids long-lived trapping of the ligand or partner proteins at nonspecific, sticky, sites on the receptor molecule and results in accelerated exploration of the possible binding regions...
2017: PloS One
https://www.readbyqxmd.com/read/28205432/fluorescent-hexose-conjugates-establish-stringent-stereochemical-requirement-by-glut5-for-recognition-and-transport-of-monosaccharides
#17
Olivier-Mohamad Soueidan, Thomas W Scully, Jatinder Kaur, Rashmi Panigrahi, Alexandr Belovodskiy, Victor Do, Carson D Matier, M Joanne Lemieux, Frank Wuest, Chris Cheeseman, F G West
The specificity characteristics of transporters can be exploited for the development of novel diagnostic therapeutic probes. The facilitated hexose transporter family (GLUTs) has a distinct set of preferences for monosaccharide substrates, and while some are expressed ubiquitously (e.g., GLUT1), others are quite tissue specific (e.g., GLUT5, which is overexpressed in some breast cancer tissues). While these differences have enabled the development of new molecular probes based upon hexose- and tissue-selective uptake, substrate design for compounds targeting these GLUT transporters has been encumbered by a limited understanding of the molecular interactions at play in hexose binding and transport...
February 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28205401/computer-aided-drug-design-to-explore-cyclodextrin-therapeutics-and-biomedical-applications
#18
Azizeh Abdolmaleki, Fatemeh Ghasemi, Jahan B Ghasemi
Cyclodextrin (CD) is a subset of the macrocyclic structural class, which is an important class of small organic agents that are useful functional excipients. They have wide range application possibilities in different fields of sciences such as material preparation, medicine, analytical chemistry, and separation processes. They are used widely in pharmaceutical formulations and drug delivery for increasing the water solubility of low soluble drugs and drug candidates. Due to the ring structure, they behave differently than smaller molecules and may be capable of hitting new classes of targets...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28198152/discovery-of-cdc25a-lead-inhibitors-with-novel-chemotype-by-virtual-screening-application-of-pharmacophore-modeling-based-on-training-set-with-unique-limited-components
#19
Yushu Ge, Qianqian Han, Wenxiu Duan, Jiaqi Zhang, Kai Chen, Jiajia Wan, Yi Liu, Dan Liu
Cdc25 phosphatase has been studied as an attractive target for cancer therapy. Multiple pharmacophore models with unique core features of classic quinone inhibitors and novel inhibitors were used to discover novel lead inhibitor. 21 compounds with qualified physical properties were screened out from Maybridge hitfinderTM database containing 14400 compounds by pharmacophore models. 4 compounds inhibit the Cdc25A activity more than 50% at concentration of 100 μM. Among them, compound KM10389 (N-(2-((furan-2-ylmethyl)thio)ethyl)-2-((4-hydroxy-6-propylpyrimidin-2-yl)thio)acetamide) shows high enzyme inhibition activity with IC₅₀ of 7...
February 14, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28198010/phenolic-1-3-diketones-attenuate-lipopolysaccharide-induced-inflammatory-response-by-an-alternative-magnesium-mediated-mechanism
#20
Morena Zusso, Giulia Mercanti, Federica Belluti, Rita Maria Concetta Di Martino, Andrea Pagetta, Carla Marinelli, Paola Brun, Eugenio Ragazzi, Rita Lo, Stefano Stifani, Pietro Giusti, Stefano Moro
BACKGROUND AND PURPOSE: Toll-like receptor 4 (TLR4) plays a key role in the induction of inflammatory responses both in peripheral organs and the CNS. Curcumin exerts anti-inflammatory functions by interfering with LPS-induced TLR4-myeloid differentiation protein-2 (MD-2) dimerization and suppressing pro-inflammatory mediator release. However, the inhibitory mechanism of curcumin remains to be defined. EXPERIMENTAL APPROACH: Binding of bis-demethoxycurcumin (GG6) and its cyclized pyrazole analogue (GG9), which lacks the 1,3-dicarbonyl function, to TLR4-MD-2 was determined using molecular docking simulations...
February 15, 2017: British Journal of Pharmacology
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