scholarly journals Theoretical study of the ligand-CYP2B4 complexes: Effect of structure on binding free energies and heme spin state

2004 ◽  
Vol 57 (3) ◽  
pp. 643-643 ◽  
Author(s):  
Danni L. Harris ◽  
Jin-Young Park ◽  
Larry Gruenke ◽  
Lucy Waskell
Keyword(s):  
Spin State ◽  
Theoretical Study ◽  
Free Energies ◽  
Effect Of Structure ◽  
Binding Free Energies

Theoretical study of the binding profile of an allosteric modulator NS-1738 with a chimera structure of the α7 nicotinic acetylcholine receptor

2016 ◽  
Vol 18 (40) ◽  
pp. 28003-28009 ◽  
Author(s):  
Guanglin Kuang ◽  
Xu Wang ◽  
Christer Halldin ◽  
Agneta Nordberg ◽  
Bengt Långström ◽  
...  
Keyword(s):  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
Theoretical Study ◽  
Allosteric Modulator ◽  
Simulation Methods ◽  
Binding Modes ◽  
Free Energies ◽  
Α7 Nicotinic Acetylcholine Receptor ◽  
Nicotinic Acetylcholine ◽  
Binding Free Energies

The binding modes and binding free energies of the allosteric modulator NS-1738 with a chimera structure of the α7 nicotinic acetylcholine receptor have been studied by molecular simulation methods.

scholarly journals Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Germano Heinzelmann ◽  
Michael K. Gilson
Keyword(s):  
Free Energy ◽  
Early Stage ◽  
Binding Free Energy ◽  
Low Cost ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Drug Candidates ◽  
Binding Free Energy Calculations ◽  
Binding Free Energies

AbstractAbsolute binding free energy calculations with explicit solvent molecular simulations can provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to find new drug candidates. However, these calculations can be complex to implement and perform. Here, we introduce the software BAT.py, a Python tool that invokes the AMBER simulation package to automate the calculation of binding free energies for a protein with a series of ligands. The software supports the attach-pull-release (APR) and double decoupling (DD) binding free energy methods, as well as the simultaneous decoupling-recoupling (SDR) method, a variant of double decoupling that avoids numerical artifacts associated with charged ligands. We report encouraging initial test applications of this software both to re-rank docked poses and to estimate overall binding free energies. We also show that it is practical to carry out these calculations cheaply by using graphical processing units in common machines that can be built for this purpose. The combination of automation and low cost positions this procedure to be applied in a relatively high-throughput mode and thus stands to enable new applications in early-stage drug discovery.

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

A computational analysis of the binding free energies of apoptosis signal-regulating kinase 1 inhibitors from different chemotypes

2021 ◽  
pp. 1-11
Author(s):  
Galyna P. Volynets ◽  
Larysa V. Pletnova ◽  
Vladislav M. Sapelkin ◽  
Oleksandr V. Savytskyi ◽  
Sergiy M. Yarmoluk
Keyword(s):  
Computational Analysis ◽  
Free Energies ◽  
Binding Free Energies

scholarly journals Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone–Wales Defects as Drug Carriers: A Molecular Dynamics Approach

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1586
Author(s):  
Leonor Contreras ◽  
Ignacio Villarroel ◽  
Camila Torres ◽  
Roberto Rozas
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Drug Delivery Systems ◽  
Nitrogen Doping ◽  
Drug Carriers ◽  
Acidic Ph ◽  
Free Energies ◽  
Interaction Forces ◽  
Chiral Nanotubes ◽  
Binding Free Energies

Doxorubicin (DOX), a recognized anticancer drug, forms stable associations with carbon nanotubes (CNTs). CNTs when properly functionalized have the ability to anchor directly in cancerous tumors where the release of the drug occurs thanks to the tumor slightly acidic pH. Herein, we study the armchair and zigzag CNTs with Stone–Wales (SW) defects to rank their ability to encapsulate DOX by determining the DOX-CNT binding free energies using the MM/PBSA and MM/GBSA methods implemented in AMBER16. We investigate also the chiral CNTs with haeckelite defects. Each haeckelite defect consists of a pair of square and octagonal rings. The armchair and zigzag CNT with SW defects and chiral nanotubes with haeckelite defects predict DOX-CNT interactions that depend on the length of the nanotube, the number of present defects and nitrogen doping. Chiral nanotubes having two haeckelite defects reveal a clear dependence on the nitrogen content with DOX-CNT interaction forces decreasing in the order 0N > 4N > 8N. These results contribute to a further understanding of drug-nanotube interactions and to the design of new drug delivery systems based on CNTs.

Theoretical study on the reduction reactions from solid char(N): The effect of the nearby group and the high-spin state

Energy ◽  
2019 ◽  
Vol 189 ◽  
pp. 116286 ◽  
Author(s):  
Hai Zhang ◽  
Lei Luo ◽  
Jiaxun Liu ◽  
Anyao Jiao ◽  
Jianguo Liu ◽  
...  
Keyword(s):  
High Spin ◽  
Spin State ◽  
Theoretical Study ◽  
High Spin State ◽  
Reduction Reactions

A Theoretical Study of Substituted Stepwise Fluorinated Cyclopropanone Keto-Enol System

2003 ◽  
Vol 58 (12) ◽  
pp. 749-755
Author(s):  
Abdullah El-Alali ◽  
Ali A. Marashdeh ◽  
Salim M. Khalil
Keyword(s):  
Theoretical Study ◽  
Dipole Moments ◽  
Heats Of Formation ◽  
Geometrical Parameters ◽  
Free Energies ◽  
Isodesmic Reactions ◽  
Orbital Energies ◽  
Substantial Concentration ◽  
Homo Lumo ◽  
Complete Optimization

MINDO-Forces calculations have been performed with complete optimization of the geometries on stepwise fluorinated cyclopropanones and their enols. Increase in the number of fluorine atoms causes destabilization of cyclopropanone. Perfluorinated enol was found to be present in substantial concentration, as was mentioned in previous work. This is supported by calculations of Gibbs free energies and isodesmic reactions. Geometrical parameters, heats of formation, electron densities, dipole moments and orbital energies (HOMO-LUMO) are reported.

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