Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment:  Implications for Structure-Based Inhibitor Design

Hwangseo Park; Sangyoub Lee

doi:10.1021/ja0304493

Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment: Implications for Structure-Based Inhibitor Design

Journal of the American Chemical Society ◽

10.1021/ja0304493 ◽

2003 ◽

Vol 125 (52) ◽

pp. 16416-16422 ◽

Cited By ~ 60

Author(s):

Hwangseo Park ◽

Sangyoub Lee

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Active Site ◽

Dynamics Simulation ◽

Inhibitor Design ◽

Protonation State ◽

Docking Experiment

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Determination of the protonation state for the catalytic dyad in β-secretase when bound to hydroxyethylamine transition state analogue inhibitors: A molecular dynamics simulation study

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2016.04.003 ◽

2016 ◽

Vol 66 ◽

pp. 155-167 ◽

Cited By ~ 6

Author(s):

Carlos Gueto-Tettay ◽

Roberto Pestana-Nobles ◽

Juan Carlos Drosos-Ramirez

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Transition State ◽

Simulation Study ◽

Dynamics Simulation ◽

Protonation State ◽

Transition State Analogue ◽

Transition State Analogue Inhibitors ◽

Catalytic Dyad

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Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-009-9267-2 ◽

2009 ◽

Vol 23 (6) ◽

pp. 375-389 ◽

Cited By ~ 13

Author(s):

Chunquan Sheng ◽

Haitao Ji ◽

Zhenyuan Miao ◽

Xiaoyin Che ◽

Jianzhong Yao ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Homology Modeling ◽

Active Site ◽

Site Characterization ◽

Dynamics Simulation ◽

Protozoan Parasites ◽

Inhibitor Design

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Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation

Journal of the American Chemical Society ◽

10.1021/ja00063a005 ◽

1993 ◽

Vol 115 (10) ◽

pp. 3883-3886 ◽

Cited By ~ 40

Author(s):

William E. Harte ◽

David L. Beveridge

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Protease Inhibitor ◽

Active Site ◽

Dynamics Simulation ◽

Protonation State ◽

Hiv 1

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Determination of potential selective inhibitors for ROCKI and ROCKII isoforms with molecular modeling techniques: structure based docking, ADMET and molecular dynamics simulation

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1491420 ◽

2018 ◽

Vol 37 (9) ◽

pp. 2457-2463 ◽

Cited By ~ 6

Author(s):

Burcu Bayel Secinti ◽

Gizem Tatar ◽

Tugba Taskin Tok

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Selective Inhibitors ◽

Modeling Techniques

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The determination of temperature stability of silver nanotubes by the molecular dynamics simulation

Applied Nanoscience ◽

10.1007/s13204-018-0770-4 ◽

2018 ◽

Vol 9 (5) ◽

pp. 853-857 ◽

Cited By ~ 1

Author(s):

O. Filatov ◽

S. Soldatenko ◽

O. Soldatenko

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Temperature Stability ◽

Dynamics Simulation ◽

Silver Nanotubes

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Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase

BMC Structural Biology ◽

10.1186/s12900-017-0075-y ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 5

Author(s):

Alexander V. Popov ◽

Anton V. Endutkin ◽

Yuri N. Vorobjev ◽

Dmitry O. Zharkov

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Active Site ◽

Dynamics Simulation ◽

Dna Glycosylase

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Determination of CO2 diffusivity in subsurface systems using molecular dynamics simulation

10.1063/5.0018070 ◽

2020 ◽

Author(s):

Oluwaseyi Aliu ◽

Hamzah Sakidin ◽

Jalal foroozesh ◽

Surajudeen Sikiru

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation

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Determination of ion quantity by using low-temperature ion density theory and molecular dynamics simulation

Chinese Physics B ◽

10.1088/1674-1056/24/11/113703 ◽

2015 ◽

Vol 24 (11) ◽

pp. 113703 ◽

Cited By ~ 1

Author(s):

Li-Jun Du ◽

Hong-Fang Song ◽

Hai-Xia Li ◽

Shao-Long Chen ◽

Ting Chen ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Low Temperature ◽

Dynamics Simulation ◽

Ion Density

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Determination of thermal conductivity of interfacial layer in nanofluids by equilibrium molecular dynamics simulation

International Journal of Heat and Mass Transfer ◽

10.1016/j.ijheatmasstransfer.2018.08.073 ◽

2019 ◽

Vol 128 ◽

pp. 199-207 ◽

Cited By ~ 10

Author(s):

Xin Wang ◽

Dengwei Jing

Keyword(s):

Thermal Conductivity ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Interfacial Layer ◽

Dynamics Simulation

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

Biointerface Research in Applied Chemistry ◽

10.33263/briac124.55915600 ◽

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.

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