Development of an RNA aptamer that acquires binding capacity against HIV-1 Tat protein via G-quadruplex formation in response to potassium ions

2017 ◽  
Vol 53 (52) ◽  
pp. 7056-7059 ◽  
Author(s):  
Yudai Yamaoki ◽  
Takashi Nagata ◽  
Tsukasa Mashima ◽  
Masato Katahira
Keyword(s):  
Binding Capacity ◽  
Binding Activity ◽  
Potassium Ions ◽  
Rna Aptamer ◽  
Tat Protein ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Target Binding ◽  
Hiv 1

The development of the first K+-responsive RNA aptamer demonstrating ON/OFF switching of its target-binding activity by sensing the addition/removal of K+ is reported.

scholarly journals HIV-1 Nucleocapsid Proteins as Molecular Chaperones for Tetramolecular Antiparallel G-Quadruplex Formation

2013 ◽  
Vol 135 (49) ◽  
pp. 18575-18585 ◽  
Author(s):  
Arivazhagan Rajendran ◽  
Masayuki Endo ◽  
Kumi Hidaka ◽  
Phong Lan Thao Tran ◽  
Jean-Louis Mergny ◽  
...  
Keyword(s):  
Molecular Chaperones ◽  
Nucleocapsid Proteins ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Hiv 1

Effects of diamond-FET-based RNA aptamer sensing for detection of real sample of HIV-1 Tat protein

2013 ◽  
Vol 40 (1) ◽  
pp. 277-282 ◽  
Author(s):  
A. Rahim Ruslinda ◽  
Kyosuke Tanabe ◽  
Shoji Ibori ◽  
Xianfen Wang ◽  
Hiroshi Kawarada
Keyword(s):  
Real Sample ◽  
Rna Aptamer ◽  
Tat Protein ◽  
Hiv 1

In vitro binding activity between HCK SH3 domain and HIV-1 Nef protein

2011 ◽  
Vol 31 (3) ◽  
pp. 262-265
Author(s):  
Xiao-lin QIN ◽  
Chao-qi LIU ◽  
Dong-ming REN ◽  
Yong-qin ZHOU
Keyword(s):  
Sh3 Domain ◽  
Binding Activity ◽  
Hiv 1

Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Arash Soltani ◽  
Seyed Isaac Hashemy ◽  
Farnaz Zahedi Avval ◽  
Houshang Rafatpanah ◽  
Seyed Abdolrahim Rezaee ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Capacity ◽  
Binding Pocket ◽  
Ligand Docking ◽  
Binding Modes ◽  
Wild Type ◽  
Parent Molecule ◽  
Discovery Studio ◽  
Approved Drugs ◽  
Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

scholarly journals Active Components from Cassia abbreviata Prevent HIV-1 Entry by Distinct Mechanisms of Action

2021 ◽  
Vol 22 (9) ◽  
pp. 5052
Author(s):  
Yue Zheng ◽  
Xian-Wen Yang ◽  
Dominique Schols ◽  
Mattia Mori ◽  
Bruno Botta ◽  
...  
Keyword(s):  
Crude Extract ◽  
Female Genital Tract ◽  
Binding Activity ◽  
Sub Saharan Africa ◽  
Active Components ◽  
Chemical Structures ◽  
3D Space ◽  
In Silico Study ◽  
Sub Saharan ◽  
Hiv 1

Cassia abbreviata is widely used in Sub-Saharan Africa for treating many diseases, including HIV-1 infection. We have recently described the chemical structures of 28 compounds isolated from an alcoholic crude extract of barks and roots ofC. abbreviata, and showed that six bioactive compounds inhibit HIV-1 infection. In the present study, we demonstrate that the six compounds block HIV-1 entry into cells: oleanolic acid, palmitic acid, taxifolin, piceatannol, guibourtinidol-(4α®8)-epiafzelechin, and a novel compound named as cassiabrevone. We report, for the first time, that guibourtinidol-(4α®8)-epiafzelechin and cassiabrevone inhibit HIV-1 entry (IC50 of 42.47 µM and 30.96 µM, respectively), as well as that piceatannol interacts with cellular membranes. Piceatannol inhibits HIV-1 infection in a dual-chamber assay mimicking the female genital tract, as well as HSV infection, emphasizing its potential as a microbicide. Structure-activity relationships (SAR) showed that pharmacophoric groups of piceatannol are strictly required to inhibit HIV-1 entry. By a ligand-based in silico study, we speculated that piceatannol and norartocarpetin may have a very similar mechanism of action and efficacy because of the highly comparable pharmacophoric and 3D space, while guibourtinidol-(4α®8)-epiafzelechin and cassiabrevone may display a different mechanism. We finally show that cassiabrevone plays a major role of the crude extract of CA by blocking the binding activity of HIV-1 gp120 and CD4.

scholarly journals DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation

2013 ◽  
Vol 41 (22) ◽  
pp. 10323-10333 ◽  
Author(s):  
Justin D. Lormand ◽  
Noah Buncher ◽  
Connor T. Murphy ◽  
Parminder Kaur ◽  
Marietta Y. Lee ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerase Δ ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Lagging Strand

HIV-1 tat protein expression in mouse brain potentiates ethanol reward and reinstates extinguished ethanol-seeking behavior

2014 ◽  
Vol 140 ◽  
pp. e141-e142
Author(s):  
Jay P. McLaughlin ◽  
M.L. Ganno ◽  
S.O. Eans ◽  
Jason J. Paris ◽  
H.D. Singh
Keyword(s):  
Protein Expression ◽  
Mouse Brain ◽  
Tat Protein ◽  
Seeking Behavior ◽  
Hiv 1
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