scholarly journals Alchemical transformations for concerted hydration free energy estimation with explicit solvation

2021 ◽  
Vol 154 (5) ◽  
pp. 054103
Author(s):  
Sheenam Khuttan ◽  
Solmaz Azimi ◽  
Joe Z. Wu ◽  
Emilio Gallicchio
Keyword(s):  
Free Energy ◽  
Hydration Free Energy ◽  
Energy Estimation ◽  
Explicit Solvation

Generalized Born implicit solvent models for small molecule hydration free energies

2017 ◽  
Vol 19 (2) ◽  
pp. 1677-1685 ◽  
Author(s):  
Martin Brieg ◽  
Julia Setzler ◽  
Steffen Albert ◽  
Wolfgang Wenzel
Keyword(s):  
Free Energy ◽  
Small Molecules ◽  
Implicit Solvent ◽  
Free Energies ◽  
Hydration Free Energy ◽  
Energy Estimation ◽  
Generalized Born ◽  
Solvent Models ◽  
Molecular Force ◽  
Implicit Solvent Models

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects.

scholarly journals Skewed thermodynamic geometry and optimal free energy estimation

2020 ◽  
Vol 153 (24) ◽  
pp. 244119
Author(s):  
Steven Blaber ◽  
David A. Sivak
Keyword(s):  
Free Energy ◽  
Energy Estimation ◽  
Thermodynamic Geometry

Can the anomalous aqueous solubility of β-cyclodextrin be explained by its hydration free energy alone?

2008 ◽  
Vol 10 (22) ◽  
pp. 3236 ◽  
Author(s):  
Wensheng Cai ◽  
Tingting Sun ◽  
Xueguang Shao ◽  
Christophe Chipot
Keyword(s):  
Free Energy ◽  
Aqueous Solubility ◽  
Hydration Free Energy

Length-Scale Dependence of Hydration Free Energy: Effect of Solute Charge

2011 ◽  
Vol 145 (2) ◽  
pp. 253-264 ◽  
Author(s):  
Jihang Wang ◽  
Dusan Bratko ◽  
Alenka Luzar
Keyword(s):  
Free Energy ◽  
Scale Dependence ◽  
Length Scale ◽  
Hydration Free Energy ◽  
Energy Effect

Docking, Binding Free Energy Estimation, and MD Simulation of Newly Designed CQ and HCQ Analogues Against the Spike-ACE2 Complex of SARS-CoV-2

2021 ◽  
Vol 6 (4) ◽  
pp. 77-89
Author(s):  
Anjoomaara H. Patel ◽  
Riya B. Patel ◽  
MahammadHussain J. Memon ◽  
Samiya S. Patel ◽  
Sharav A. Desai ◽  
...  
Keyword(s):  
Free Energy ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Docking Studies ◽  
Radius Of Gyration ◽  
Ligand Interaction ◽  
Energy Estimation ◽  
Efficacious Treatment ◽  
Protein Ligand Interaction ◽  
Derivatives Of

The coronavirus disease 2019 (COVID-19) virus has been spreading rapidly, and scientists are endeavouring to discover drugs for its efficacious treatment. Chloroquine phosphate, an old drug for treatment of malaria, has shown to have apparent efficacy and acceptable safety against COVID-19. As a part of Drug Discovery Hackathon-2020, in this study, the authors have tried making the derivatives of CQ and HCQ using MarvinSketch by ChemAxon. Molecular docking studies of these ligands were performed using Glide by Schrodinger, and ADME profiles were obtained by using QikProp. The obtained results after data analysis demonstrated that ligands HCQ_imidazoll, choloroquine_3c, HCQ_pyrrolC had good binding affinity and complied with all the ADME parameters. The molecular dynamic simulation of these ligands in complex with the 2019-nCoV RBD/ACE-2-B0AT1 complex PDB ID: 6M17 were carried out, and the parameters like RMSD, RMSF, and radius of gyration were observed to understand the fluctuations and protein-ligand interaction.

A simple COSMO-based method for calculation of hydration energies of neutral molecules

2019 ◽  
Vol 21 (34) ◽  
pp. 18706-18713 ◽  
Author(s):  
Alexander A. Voityuk ◽  
Sergei F. Vyboishchikov
Keyword(s):  
Free Energy ◽  
Accurate Method ◽  
Hydration Free Energy ◽  
Hydration Energies

A simple yet accurate method to estimate hydration free energy of neutral molecules is developed.

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