Computer Assisted EPR Spectroscopy, with Applications to Inter- and Intra-Molecular Dynamics of Radicals in Solution

1986 ◽  
pp. 437-461
Author(s):  
M. Barzaghi ◽  
M. Branca ◽  
A. Gamba ◽  
C. Oliva ◽  
M. Simonetta
Keyword(s):  
Molecular Dynamics ◽  
Epr Spectroscopy ◽  
Computer Assisted

Molecular dynamics simulation and EPR spectroscopy of nitroxide side chains in bacteriorhodopsin

2000 ◽  
Vol 84 (1) ◽  
pp. 17-27 ◽  
Author(s):  
Heinz-Jürgen Steinhoff ◽  
Matthias Müller ◽  
Christian Beier ◽  
Matthias Pfeiffer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Epr Spectroscopy ◽  
Dynamics Simulation ◽  
Side Chains

scholarly journals Docking of FDA Approved Drugs Targeting NSP-16, N-Protein and Main Protease of SARS-CoV-2 as Dual Inhibitors

2020 ◽  
Vol 11 (3) ◽  
pp. 9848-9861
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
High Throughput Screening ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Structural Proteins ◽  
Computer Assisted ◽  
Dual Inhibitor ◽  
N Protein ◽  
Dual Inhibitors

At present world is lurching under the spread of new SARS-CoV-2 infection. The treatment is still elusive despite the relentless effort by the scientists against various viral structures. Whereas the 3-Chymotrypsin-like proteases cleave polyproteins and structural proteins help in viral replication. At the same time, non-structural proteins stimulate mRNA cap methylation to evade the immune response. The present study aims to identify novel dual inhibitor compounds with potential hits simultaneously against any of these three targets, including 3C-like proteases, N-protein, and NSP16 through virtual screening, molecular docking approach, and molecular dynamics. Such dual inhibitors may provide the necessary treatment to alleviate the current pandemic. We screened 265 FDA approved infectious disease drugs against three types of Covid-19 targets, i.e., 3C-like proteinase (6w63), N-protein (6vyo), and Non-structural protein 16 (6w4h) using a computer-assisted drug repurposing approach in this study. The Schrodinger suite 2019 is employed for high throughput screening, molecular docking, and binding free energy through the Glide module. We sorted 27 drugs, out of which the best common three drugs were suggested based on their virtual statistics parameters. We found three drugs that belonged to two main categories as dual inhibitors. The Plazomicin (Aminoglycoside) and Cefiderocol (Cephalosporins) are an antibiotic group of drugs, and the Vanganciclovir is antiviral. The molecular dynamics simulation studies over 30000ps for Plazomicin against NSP16 was conducted based on their promising docking scores profile. The RMSD parameter remained stable at 2.5Å for ligands for 30000ps. Thus these three compounds can be validated as a SARS-CoV-2 therapy through clinical trials.

scholarly journals Lipid dynamics in nanoparticles formed by maleic acid-containing copolymers: EPR spectroscopy and molecular dynamics simulations

2020 ◽  
Vol 1862 (5) ◽  
pp. 183207 ◽  
Author(s):  
Alexandr Colbasevici ◽  
Natalia Voskoboynikova ◽  
Philipp S. Orekhov ◽  
Marine E. Bozdaganyan ◽  
Maria G. Karlova ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Epr Spectroscopy ◽  
Maleic Acid ◽  
Lipid Dynamics ◽  
Dynamics Simulations

Amplitude of Pancreatic Lipase Lid Opening in Solution and Identification of Spin Label Conformational Subensembles by Combining Continuous Wave and Pulsed EPR Spectroscopy and Molecular Dynamics

Biochemistry ◽  
2010 ◽  
Vol 49 (10) ◽  
pp. 2140-2149 ◽  
Author(s):  
Sebastien Ranaldi ◽  
Valérie Belle ◽  
Mireille Woudstra ◽  
Raphael Bourgeas ◽  
Bruno Guigliarelli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pancreatic Lipase ◽  
Epr Spectroscopy ◽  
Spin Label ◽  
Continuous Wave ◽  
Pulsed Epr

The Investigation of Molecular Dynamics in Pyridinium Perchlorate Single Crystal by CW-EPR Spectroscopy Combined with Computer Resolution Enhancement Method

2002 ◽  
Vol 75 (4-5) ◽  
pp. 379-388
Author(s):  
Ryszard Krzyminiewski ◽  
RadosŁaw MichaŁ Kowalczyk ◽  
Piotr Czarnecki ◽  
Hanna MaŁuszyńska
Keyword(s):  
Molecular Dynamics ◽  
Single Crystal ◽  
Epr Spectroscopy ◽  
Resolution Enhancement ◽  
Enhancement Method ◽  
Pyridinium Perchlorate
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