Molecular dynamics simulation of the enhancement of cobra cardiotoxin and E6 protein binding on mixed self-assembled monolayer molecules

Comparative molecular similarity index analysis (CoMSIA) was used to establish a three-dimensional quantitative structure–activity relationship (3D-QSAR) model with structural parameters of quinolones as the independent variables and plasma protein binding rate (logfb) as the dependent variable to predict the logfb values of remaining quinolones in this study. In addition, the mono-substituted and bis-substituted reaction schemes that significantly influenced the plasma protein binding rate of quinolones were determined through an analysis of the 3D-QSAR contour maps. It was found that the replacement of small groups, hydrophobic groups, electronegative groups, or hydrogen bond acceptor groups at the substitution sites significantly reduce the logfb values of quinolone derivatives. Furthermore, the mechanism of decrease in binding rate between trovafloxacin (TRO) derivatives and plasma protein was revealed qualitatively and quantitatively based on molecular docking and molecular dynamics simulation. After modification of the target molecule, 11 TRO derivatives with low plasma protein binding rates were screened (reduced by 0.50–24.18%). Compared with the target molecule, the molecular genotoxicity and photodegradability of the TRO derivatives was higher (genotoxicity increased by 4.89–21.36%, and photodegradability increased by 9.04–20.56%), and their bioconcentration was significantly lower (by 36.90–61.41%).

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Preferable Molecular Orientation of Poly(3-hexylthiophene) on Self-Assembled Monolayers: Molecular Dynamics Simulation

Molecular Crystals and Liquid Crystals ◽

10.1080/15421406.2013.803416 ◽

2013 ◽

Vol 578 (1) ◽

pp. 33-36 ◽

Cited By ~ 1

Author(s):

Shigeaki Obata ◽

Yukihiro Shimoi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Molecular Orientation ◽

Dynamics Simulation ◽

Self Assembled Monolayers ◽

Assembled Monolayers ◽

Self Assembled

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Molecular dynamics simulation of self-assembled nanocubes in methanol

Molecular Simulation ◽

10.1080/08927022.2014.940523 ◽

2014 ◽

Vol 41 (10-12) ◽

pp. 845-849 ◽

Cited By ~ 2

Author(s):

Takako Mashiko ◽

Kenta Yamada ◽

Shuichi Hiraoka ◽

Umpei Nagashima ◽

Masanori Tachikawa

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Self Assembled

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Effect of Pressure on Dry and Hydrated Self Assembled Monolayers: A Molecular Dynamics Simulation Study

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.553.35 ◽

2014 ◽

Vol 553 ◽

pp. 35-40

Author(s):

Leyla Ramin ◽

Ahmad Jabbarzadeh

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

High Pressures ◽

Elastic Recovery ◽

Structural Characteristics ◽

Dynamics Simulation ◽

Self Assembled Monolayers ◽

Effect Of Pressure ◽

Assembled Monolayers ◽

Self Assembled

Molecular dynamics simulation was used to study the effect of pressure on self-assembled monolayers (SAM) of n-alkanethiols [(CH3(CH2) n-1, n=14, 15] on Au (111) for dry systems and in the presence of water. The stress-strain behavior and effects of compression on structural characteristics under various normal pressures have been investigated. We found the effect of compression on tilt and tilt orientation angles for dry and hydrated SAM system. Furthermore, a comparison of the results obtained for tilt and tilt orientation angles for hydrated C14 and C15 indicates a more stable structure for C15 (an odd system) under high pressures. We also found excellent elastic recovery of SAM monolayers with and without water is evidence of their exceptional potential to be used under compression in various conditions. Young’s moduli are calculated for various systems under uniaxial compression.

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