scholarly journals Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method

2004 ◽  
Vol 25 (16) ◽  
pp. 2049-2064 ◽  
Author(s):  
Ninad V. Prabhu ◽  
Peijuan Zhu ◽  
Kim A. Sharp
Keyword(s):  
Molecular Dynamics ◽  
Finite Difference ◽  
Implicit Solvation ◽  
Poisson Boltzmann ◽  
Boltzmann Method

scholarly journals An improved pairwise decomposable finite-difference Poisson–Boltzmann method for computational protein design

2008 ◽  
Vol 29 (7) ◽  
pp. 1153-1162 ◽  
Author(s):  
Christina L. Vizcarra ◽  
Naigong Zhang ◽  
Shannon A. Marshall ◽  
Ned S. Wingreen ◽  
Chen Zeng ◽  
...  
Keyword(s):  
Finite Difference ◽  
Protein Design ◽  
Computational Protein Design ◽  
Poisson Boltzmann ◽  
Boltzmann Method

scholarly journals Explanation of the Formation of Complexes between Representatives of Oxazolidinones and HDAS-β-CD Using Molecular Modeling as a Complementary Technique to cEKC and NMR

2021 ◽  
Vol 22 (13) ◽  
pp. 7139
Author(s):  
Wojciech Bocian ◽  
Elżbieta Bednarek ◽  
Katarzyna Michalska
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Chiral Separation ◽  
Structural Information ◽  
Binding Constants ◽  
Nmr Studies ◽  
Thermodynamics Of Complexation ◽  
Poisson Boltzmann ◽  
Explicit Water

Molecular modeling (MM) results for tedizolid and radezolid with heptakis-(2,3-diacetyl-6-sulfo)-β-cyclodextrin (HDAS-β-CD) are presented and compared with the results previously obtained for linezolid and sutezolid. The mechanism of interaction of chiral oxazolidinone ligands belonging to a new class of antibacterial agents, such as linezolid, tedizolid, radezolid, and sutezolid, with HDAS-β-CD based on capillary electrokinetic chromatography (cEKC), nuclear magnetic resonance (NMR) spectroscopy, and MM methods was described. Principles of chiral separation of oxazolidinone analogues using charged single isomer derivatives of cyclodextrin by the cEKC method were presented, including the selection of the optimal chiral selector and separation conditions, complex stoichiometry, and binding constants, which provided a comprehensive basis for MM studies. In turn, NMR provided, where possible, direct information on the geometry of the inclusion complexes and also provided the necessary structural information to validate the MM calculations. Consequently, MM contributed to the understanding of the structure of diastereomeric complexes, the thermodynamics of complexation, and the visualization of their structures. The most probable mean geometries of the studied supramolecular complexes and their dynamics (geometry changes over time) were determined by molecular dynamics methods. Oxazolidinone ligands have been shown to complex mainly the inner part of cyclodextrin, while the external binding is less privileged, which is consistent with the conclusions of the NMR studies. Enthalpy values of binding of complexes were calculated using long-term molecular dynamics in explicit water as well as using molecular mechanics, the Poisson–Boltzmann or generalized Born, and surface area continuum solvation (MM/PBSA and MM/GBSA) methods. Computational methods predicted the effect of changes in pH and composition of the solution on the strength and complexation process, and it adapted the conditions selected as optimal during the cEKC study. By changing the dielectric constant in the MM/PBSA and MM/GBSA calculations, the effect of changing the solution to methanol/acetonitrile was investigated. A fairly successful attempt was made to predict the chiral separation of the oxazolidinones using the modified cyclodextrin by computational methods.

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