keyword
MENU ▼
Read by QxMD icon Read
search

Docking

keyword
https://www.readbyqxmd.com/read/29353314/robot-assisted-post-chemotherapy-retroperitoneal-lymph-node-dissection-in-germ-cell-tumor-is-the-single-docking-with-lateral-approach-relevant
#1
C Overs, J B Beauval, L Mourey, P Rischmann, M Soulié, M Roumiguié, Nicolas Doumerc
INTRODUCTION: Surgical treatment of post-chemotherapy residual mass of germ cell tumor (GCT) may be performed in various techniques. We assess the feasibility, safety, and efficacy of single-docking with lateral approach robot-assisted retroperitoneal lymph node dissection (R-RPLND) in residual mass of GCT in our center. MATERIALS AND METHODS: A retrospective review of patients undergoing R-RPLND for residual mass of CGT was performed between January 2014 and April 2017...
January 20, 2018: World Journal of Urology
https://www.readbyqxmd.com/read/29352977/paclitaxel-inhibited-lysozyme-fibrillation-by-increasing-colloidal-stability-through-formation-of-off-pathway-oligomers
#2
Ehsan Kachooei, Faroogh Mozaffarian, Fariba Khodagholi, Payam Sedeghi, Leila Karami, Atiyeh Ghasemi, Elham Vahdat, Ali Akbar Saboury, Nader Sheibani, Ali Akbar Moosavi-Movahedi
Protein fibrillation is a challenging issue in medicine, causing many diseases, and an impediment to pharmaceutics and protein industry. Many chemicals, especially polyphenol compounds and aromatic small molecules, have been widely used as an effective strategy to combat protein fibril formation. Hence, understanding mechanisms of fibrillation inhibition and contributing forces in this process are significant. In this study, the inhibitory effect of paclitaxel on lysozyme fibrillation was investigated with respect to thermal and colloidal stability...
January 15, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29352942/comparative-study-of-molecular-recognition-of-folic-acid-subunits-with-cyclodextrins
#3
Magdalena Ceborska, Karolina Kędra-Królik, Aneta Aniela Kowalska, Małgorzata Koźbiał
The complexation of pteroic acid and pterine, subunits of folic acid, with native cyclodextrins (α‒, β‒, and γ‒CDs) was studied in solution (UV-vis), and in the solid state (thermal analysis, IR and Raman). UV-vis titrations at pH = 7.4 provided data regarding stoichiometry of the formed complexes as well as their associations constants. Stability of the complexes increases in the series: γ‒CD < β‒CD < α‒CD for pterine, and γ‒CD < α‒CD < β‒CD for pteroic acid...
March 15, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29352270/non-canonical-wnt-induces-chondrocyte-de-differentiation-through-frizzled-6-and-dvl-2-b-raf-camkii%C3%AE-syndecan-4-axis
#4
Zhe Xie, Mostafa Khair, Irfan Shaukat, Patrick Netter, Didier Mainard, Lydia Barré, Mohamed Ouzzine
Dysregulation of Wnt signaling has been implicated in developmental defects and in the pathogenesis of many diseases such as osteoarthritis; however, the underlying mechanisms are poorly understood. Here, we report that non-canonical Wnt signaling induced loss of chondrocyte phenotype through activation of Fz-6/DVL-2/SYND4/CaMKIIα/B-raf/ERK1/2 cascade. We show that in response to Wnt-3a, Frizzled 6 (Fz-6) triggers the docking of CaMKIIα to syndecan 4 (SYND4) and that of B-raf to DVL-2, leading to the phosphorylation of B-raf by CaMKIIα and activation of extracellular signal-regulated kinase 1 and 2 (ERK1/2) signaling, which leads to chondrocyte de-differentiation...
January 19, 2018: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29352227/ly2087101-and-dfbr-share-transmembrane-binding-sites-in-the-%C3%AE-4-3-%C3%AE-2-2-nicotinic-acetylcholine-receptor
#5
Farah Deba, Hamed I Ali, Abisola Tairu, Kara Ramos, Jihad Ali, Ayman K Hamouda
Positive allosteric modulators (PAMs) of nicotinic acetylcholine receptors (nAChRs) have potential therapeutic application in neuropathologies associated with decrease in function or loss of nAChRs. In this study, we characterize the pharmacological interactions of the nAChRs PAM, LY2087101, with the α4β2 nAChR using mutational and computational analyses. LY2087101 potentiated ACh-induced currents of low-sensitivity (α4)3(β2)2 and high-sensitivity (α4)2(β2)3 nAChRs with similar potencies albeit to a different maximum potentiation (potentiation I max  = ~840 and 450%, respectively)...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29351887/synthesis-and-anti-tumor-activity-of-ef24-analogues-as-ikk%C3%AE-inhibitors
#6
Rong Jin, Qiuxiang Chen, Song Yao, Encheng Bai, Weitao Fu, Ledan Wang, Jiabing Wang, Xiaojing Du, Tao Wei, Haineng Xu, Chengxi Jiang, Peihong Qiu, Jianzhang Wu, Wulan Li, Guang Liang
EF24 is an IKKβ inhibitor (IC50: 72 μM) containing various anti-tumor activities. In this study, a series of EF24 analogs targeting IKKβ were designed and synthesized. Several IKKβ inhibitors with better activities than EF24 were screened out and B3 showed best IKKβ inhibitory (IC50: 6.6 μM). Molecular docking and dynamic simulation experiments further confirmed this inhibitory effect. B3 obviously suppressed the viability of Hela229, A549, SGC-7901 and MGC-803 cells. Then, in SGC-7901 and MGC-803 cells, B3 blocked the NF-κB signal pathway by inhibiting IKKβ phosphorylation, and followed arrested the cell cycle at G2/M phase by suppressing the Cyclin B1 and Cdc2 p34 expression, induced the cell apoptosis by down-regulating Bcl-2 protein and up-regulating cleaved-caspase3...
December 7, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29351717/prediction-of-protein-configurational-entropy-popcoen
#7
Martin Goethe, Jan Gleixner, Ignacio Fita, J Miguel Rubi
A knowledge-based method for configurational entropy prediction of proteins is presented which is extremely fast compared to previous approaches because it does not involve any kind of configurational sampling. Instead, the configurational entropy of a query fold is estimated by evaluating an artificial neural network which was trained on molecular-dynamics simulations of about 1000 proteins. The predicted entropy can be incorporated into a large class of protein software based on cost-function minimization/evaluation in which configurational entropy is currently neglected for performance reasons...
January 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29351374/fast-dynamic-docking-guided-by-adaptive-electrostatic-bias-the-md-binding-approach
#8
Andrea Spitaleri, Sergio Decherchi, Andrea Cavalli, Walter Rocchia
Engineering chemical entities to modify how pharmaceutical targets function, as it is done in drug design, requires a good understanding of molecular recognition and binding. In this context, the limitations of statically describing bimolecular recognition, as done in docking/scoring, call for insightful and efficient dynamical investigations. On the experimental side, the characterization of dynamical binding processes is still in its infancy. Thus, computer simulations, particularly molecular dynamics (MD), are compelled to play a prominent role, allowing a deeper comprehension of the binding process and its causes and thus a more informed compound selection, making more significant the computational contribution to drug discovery1...
January 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29349513/3d-qsar-study-of-steroidal-and-azaheterocyclic-human-aromatase-inhibitors-using-quantitative-profile-of-protein-ligand-interactions
#9
Sehan Lee, Mace G Barron
Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, including sexual differentiation and maturation, aromatase is a potential target for endocrine disrupting chemicals as well as breast cancer therapy. In this work, 3D-QSAR combined with quantitative profile of protein-ligand interactions was employed in the identification and characterization of critical steric and electronic features of aromatase-inhibitor complexes and the estimation of their quantitative contribution to inhibition potency...
January 18, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29349448/a-study-on-platinum-iv-species-containing-an-estrogen-receptor-modulator-to-reverse-tamoxifen-resistance-of-breast-cancer
#10
Weiwei Hu, Jian Zhao, Wuyang Hua, Shaohua Gou
Several dual-action Tam-Pt(iv) complexes derived from tamoxifen (Tam) and platinum(ii) drugs were designed and synthesized for targeting estrogen receptors (ERs) and DNA. These novel compounds not only exhibited potent cytotoxicity against breast cancer cells, but also reversed the tamoxifen resistance of TamR-MCF-7 cancer cells. Computational docking assays together with cellular uptake data demonstrated that the ER ligand portion of these conjugates plays a targeting role in ER-positive tumor cells and promotes the uptake of platinum via an estrogen receptor-mediated pathway...
January 19, 2018: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29349445/discovery-of-novel-diarylpyrimidines-as-potent-hiv-1-nnrtis-by-investigating-the-chemical-space-of-a-less-explored-hydrophobic-channel
#11
Zhongxia Zhou, Tao Liu, Dongwei Kang, Zhipeng Huo, Gaochan Wu, Dirk Daelemans, Erik De Clercq, Christophe Pannecouque, Peng Zhan, Xinyong Liu
A new series of diarylpyrimidines (DAPYs) were designed, synthesized and evaluated as novel HIV-1 NNRTIs to further explore the chemical space surrounding the "hydrophobic channel" of the NNRTI binding pocket (NNIBP), guided by the comprehensive analysis of X-ray structural biology data of HIV-1 RT/NNRTI complexes and molecular modeling. Encouragingly, most of the synthesized DAPYs were found to be active against the HIV-1 wild-type (WT) strain with EC50 values ranging from 3 nM to 63 nM, and displayed significantly reduced cytotoxicity compared with etravirine (ETV) and rilpivirine (RPV)...
January 19, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29349002/medial-patellofemoral-ligament-reconstruction-using-dual-patella-docking-technique
#12
Hassan Azimi, Oke Anakwenze
Medial patellofemoral ligament (MPFL) injuries are common in children and young adults. In patients with recurrent patellar dislocations with normal lower-extremity alignment, anatomic reconstruction of the MPFL has been shown to restore patellar stability. We describe a technique that creates an anatomic reconstruction using a dual docking technique into the patella. Our technique is simple and efficacious for reconstructing the MPFL without implant fixation in the patella, allowing a maximal bone-tendon interface for healing...
December 2017: Arthroscopy Techniques
https://www.readbyqxmd.com/read/29348648/specific-cyclic-adp-ribose-phosphohydrolase-obtained-by-mutagenic-engineering-of-mn2-dependent-adp-ribose-cdp-alcohol-diphosphatase
#13
João Meireles Ribeiro, José Canales, Alicia Cabezas, Joaquim Rui Rodrigues, Rosa María Pinto, Iralis López-Villamizar, María Jesús Costas, José Carlos Cameselle
Cyclic ADP-ribose (cADPR) is a messenger for Ca2+ mobilization. Its turnover is believed to occur by glycohydrolysis to ADP-ribose. However, ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cADPR phosphohydrolase with much lower efficiency than on its major substrates. Recently, we showed that mutagenesis of human ADPRibase-Mn at Phe37, Leu196 and Cys253 alters its specificity: the best substrate of the mutant F37A + L196F + C253A is cADPR by a short difference, Cys253 mutation being essential for cADPR preference...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348557/sensitizing-tumor-cells-to-conventional-drugs-hsp70-chaperone-inhibitors-their-selection-and-application-in-cancer-models
#14
Vladimir F Lazarev, Dmitry V Sverchinsky, Elena R Mikhaylova, Pavel I Semenyuk, Elena Y Komarova, Sergey A Niskanen, Alina D Nikotina, Anton V Burakov, Viktor G Kartsev, Irina V Guzhova, Boris A Margulis
Hsp70 chaperone controls proteostasis and anti-stress responses in rapidly renewing cancer cells, making it an important target for therapeutic compounds. To date several Hsp70 inhibitors are presented with remarkable anticancer activity, however their clinical application is limited by the high toxicity towards normal cells. This study aimed to develop assays to search for the substances that reduce the chaperone activity of Hsp70 and diminish its protective function in cancer cells. On our mind the resulting compounds alone should be safe and function in combination with drugs widely employed in oncology...
January 18, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29348555/novel-immunoinformatics-approaches-to-design-multi-epitope-subunit-vaccine-for-malaria-by-investigating-anopheles-salivary-protein
#15
Rajan Kumar Pandey, Tarun Kumar Bhatt, Vijay Kumar Prajapati
Malaria fever has been pervasive for quite a while in tropical developing regions causing high morbidity and mortality. The causal organism is a protozoan parasite of genus Plasmodium which spreads to the human host by the bite of hitherto infected female Anopheles mosquito. In the course of biting, a salivary protein of Anopheles helps in blood feeding behavior and having the ability to elicit the host immune response. This study represents a series of immunoinformatics approaches to design multi-epitope subunit vaccine using Anopheles mosquito salivary proteins...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348410/oxidative-stress-via-inhibition-of-the-mitochondrial-electron-transport-and-nrf-2-mediated-anti-oxidative-response-regulate-the-cytotoxic-activity-of-plumbagin
#16
Arvinder Kapur, Thomas Beres, Kavya Rathi, Amruta P Nayak, Austin Czarnecki, Mildred Felder, Amani Gillette, Spencer S Ericksen, Emmanuel Sampene, Melissa C Skala, Lisa Barroilhet, Manish S Patankar
Plumbagin, an anti-cancer agent, is toxic to cells of multiple species. We investigated if plumbagin targets conserved biochemical processes. Plumbagin induced DNA damage and apoptosis in cells of diverse mutational background with comparable potency. A 3-5 fold increase in intracellular oxygen radicals occurred in response to plumbagin. Neutralization of the reactive oxygen species by N-acetylcysteine blocked apoptosis, indicating a central role for oxidative stress in plumbagin-mediated cell death. Plumbagin docks in the ubiquinone binding sites (Q0 and Qi) of mitochondrial complexes I-III, the major sites for oxygen radicals...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348046/synthesis-of-sulfamide-analogues-of-deoxthymidine-monophosphate-as-potential-inhibitors-of-mycobacterial-cell-wall-biosynthesis
#17
Kajitha Suthagar, Wanting Jiao, Hélène Munier-Lehmann, Antony J Fairbanks
The recently discovered enzyme Mycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt), which catalyses the phosphorylation of deoxythymidine monophosphate (dTMP) to give deoxythymidine diphosphate (dTDP), is indispensable for the growth and survival of M. tuberculosis as it plays an essential role in DNA synthesis. Inhibition of TMPKmt is an attractive avenue for the development of novel anti-tuberculosis agents. Based on the premise that sulfamide may be a suitable isostere of phosphate, deoxythymidine analogues comprising various substituted sulfamides at C5' were modelled in silico into the active site of TMPKmt (PDB accession code: 1N5K) using induced-fit docking methods...
January 11, 2018: Carbohydrate Research
https://www.readbyqxmd.com/read/29347844/docking-analysis-targeted-to-the-whole-enzyme-an-application-to-the-prediction-of-inhibition-of-ptp1b-by-thiomorpholine-and-thiazolyl-derivatives
#18
C A Ganou, P Th Eleftheriou, P Theodosis-Nobelos, M Fesatidou, A A Geronikaki, T Lialiaris, E A Rekka
PTP1b is a protein tyrosine phosphatase involved in the inactivation of insulin receptor. Since inhibition of PTP1b may prolong the action of the receptor, PTP1b has become a drug target for the treatment of type II diabetes. In the present study, prediction of inhibition using docking analysis targeted specifically to the active or allosteric site was performed on 87 compounds structurally belonging to 10 different groups. Two groups, consisting of 15 thiomorpholine and 10 thiazolyl derivatives exhibiting the best prediction results, were selected for in vitro evaluation...
February 2018: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29346393/computational-study-of-hiv-gp120-as-a-target-for-polyanionic-entry-inhibitors-exploiting-the-v3-loop-region
#19
Louis R Hollingsworth, Anne M Brown, Richard D Gandour, David R Bevan
Multiple approaches are being utilized to develop therapeutics to treat HIV infection. One approach is designed to inhibit entry of HIV into host cells, with a target being the viral envelope glycoprotein, gp120. Polyanionic compounds have been shown to be effective in inhibiting HIV entry, with a mechanism involving electrostatic interactions with the V3 loop of gp120 being proposed. In this study, we applied computational methods to elucidate molecular interactions between the repeat unit of the precisely alternating polyanion, Poly(4,4'-stilbenedicarboxylate-alt-maleic acid) (DCSti-alt-MA) and the V3 loop of gp120 from strains of HIV against which these polyanions were previously tested (IIIb, BaL, 92UG037, JR-CSF) as well as two strains for which gp120 crystal structures are available (YU2, 2B4C)...
2018: PloS One
https://www.readbyqxmd.com/read/29346072/synthesis-biological-evaluation-and-molecular-docking-studies-of-novel-benzimidazole-derivatives
#20
Gagandeep Singh, Amanjot Singh, Raman K Verma, Rajiv Mall, Uzma Azeem
A novel series of N-substituted-benzimidazolyl linked para substituted benzylidene based molecules containing three pharmacologically potent hydrogen bonding parts namely; 2,4-thiazolidinedione (TZD: a 2,4-dicarbonyl), diethyl malonate (DEM: a 1,3-diester and an isooxazolidinedione analog) and methyl acetoacetate (MAA: a β-ketoester) (6a-11b) were synthesized and evaluated for in vitro α-glucosidase inhibition. The structure of the novel synthesized compounds was confirmed through the spectral studies (LC-MS, 1H NMR, 13C NMR, FT-IR)...
December 30, 2017: Computational Biology and Chemistry
keyword
keyword
84854
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"