scholarly journals Active-site residues move independently from the rest of the protein in a 200ns molecular dynamics simulation of cytochrome P450 CYP119

2011 ◽  
Vol 509 (2) ◽  
pp. 127-132 ◽  
Author(s):  
Relly Brandman ◽  
Jed N. Lampe ◽  
Yigal Brandman ◽  
Paul R. Ortiz de Montellano
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome P450 ◽  
Molecular Dynamics Simulation ◽  
Active Site ◽  
Dynamics Simulation ◽  
Active Site Residues

Insight into the Interaction Mechanism of Nicotine, NNK, and NNN with Cytochrome P450 2A13 Based on Molecular Dynamics Simulation

2019 ◽  
Vol 60 (2) ◽  
pp. 766-776 ◽  
Author(s):  
Jorddy Neves Cruz ◽  
Mozaniel Santana de Oliveira ◽  
Sebastião Gomes Silva ◽  
Antonio Pedro da Silva Souza Filho ◽  
Daniel Santiago Pereira ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome P450 ◽  
Molecular Dynamics Simulation ◽  
Interaction Mechanism ◽  
Dynamics Simulation ◽  
Insight Into

scholarly journals Molecular Docking and Molecular Dynamics Studies of SARS-CoV-2 Inhibitors: Crocin, Digitoxigenin, Beta-Eudesmol and Favipiravir: Comparative Study

2021 ◽  
Vol 12 (4) ◽  
pp. 5591-5600
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Comparative Study ◽  
Active Site ◽  
Antiviral Treatment ◽  
Docking Study ◽  
The Other ◽  
Dynamics Simulation ◽  
Main Protease

In this study, Crocin, Digitoxigenin, Beta-Eudesmol, and Favipiravir were docked in the active site of SARS-CoV-2 main protease (PDB code: 6LU7). The docking study was followed by Molecular Dynamics simulation. The result indicates that Crocin and Digitoxigenin are the structures with the best affinity in the studied enzyme's binding site. Still, Molecular Dynamics simulation showed that Digitoxigenin is the molecule that fits better in the active site of the main protease. Therefore, this molecule could have a more potent antiviral treatment of COVID-19 than the other three studied compounds.

TOWARD A BLUEPRINT FOR β-PRIMEVEROSIDASE FROM TEA LEAVES STRUCTURE/FUNCTION PROPERTIES: HOMOLOGY MODELING STUDY

2006 ◽  
Vol 05 (spec01) ◽  
pp. 433-446 ◽  
Author(s):  
WEI-WEI HAN ◽  
ZE-SHENG LI ◽  
QING-CHUAN ZHENG ◽  
CHIA-CHUNG SUN
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Homology Modeling ◽  
Active Site ◽  
3D Model ◽  
Dynamics Simulation ◽  
Experimental Investigations ◽  
Refined Model ◽  
Tea Leaves ◽  
Final Model

By means of the Homology modeling and the known structure of cyannogenic β-glycosidase from white clover (1CBG, EC 3.2.1.21), we construct a 3D model of the β-primeverosidase (EC 3.2.1.149) and search for the binding site of substrate. The 3D model is then refined by using molecular mechanics (optimization and molecular dynamics) simulation. Finally, the refined model is further assessed by Profile-3D and PROCHECK, and the results showed that the final model is reliable. Furthermore, the docking of the substrates into the active site of the protein indicates that β-primeverosidase is able to hydrolyze β-primeverosides, but not act on 2-phenylethyl β-D-glucopyranoside. These results suggest that β-primeverosidase shows broad substrate specificity with respect to the disaccharide glycon moiety (subsite -2). This is consistent with the experimental observation. Thr271 and Thr415 play important roles in subsite -2 of β-primeverosidase. Our results may be helpful for further experimental investigations.

scholarly journals Structure-Based Drug Design Studies Toward the Discovery of Novel Chalcone Derivatives as Potential Epidermal Growth Factor Receptor (EGFR) Inhibitors

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3203 ◽  
Author(s):  
Menier Al-Anazi ◽  
Belal Al-Najjar ◽  
Melati Khairuddean
Keyword(s):  
Molecular Dynamics ◽  
Epidermal Growth Factor Receptor ◽  
Molecular Dynamics Simulation ◽  
Growth Factor ◽  
Epidermal Growth Factor ◽  
Active Site ◽  
Growth Factor Receptor ◽  
Dynamics Simulation ◽  
Chalcone Derivatives ◽  
Epidermal Growth

Human Epidermal Growth Factor Receptor-1 (EGFR), a transmembrane tyrosine kinase receptor (RTK), has been associated with several types of cancer, including breast, lung, ovarian, and anal cancers. Thus, the receptor was targeted by a variety of therapeutic approaches for cancer treatments. A series of chalcone derivatives are among the most highly potent and selective inhibitors of EGFR described to date. A series of chalcone derivatives were proposed in this study to investigate the intermolecular interactions in the active site utilizing molecular docking and molecular dynamics simulations. After a careful analysis of docking results, compounds 1a and 1d were chosen for molecular dynamics simulation study. Extensive hydrogen bond analysis throughout 7 ns molecular dynamics simulation revealed the ability of compounds 1a and 1d to retain the essential interactions needed for the inhibition, especially MET 93. Finally, MM-GBSA calculations highlight on the capability of the ligands to bind strongly within the active site with binding energies of −44.04 and −56.6 kcal/mol for compounds 1a and 1d, respectively. Compound 1d showed to have a close binding energy with TAK-285 (−66.17 kcal/mol), which indicates a high chance for compound 1d to exhibit inhibitory activity, thus recommending to synthesis it to test its biological activity. It is anticipated that the findings reported here may provide very useful information for designing effective drugs for the treatment of EGFR-related cancer disease.

scholarly journals Protein dynamics of active site studied by the molecular dynamics simulation.

2003 ◽  
Vol 43 (supplement) ◽  
pp. S54
Author(s):  
Atushi T. ◽  
H. Nakagawa ◽  
H. Kamikubo ◽  
Y. Joti ◽  
A. Kitao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Protein Dynamics ◽  
Active Site ◽  
Dynamics Simulation
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