Literature DB >> 26615695

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model.

Christopher R Corbeil1, Traian Sulea1, Enrico O Purisima1.   

Abstract

Local ordering of water in the first hydration shell around a solute is different from isotropic bulk water. This leads to effects that are captured by explicit solvation models and missed by continuum solvation models which replace the explicit waters with a continuous medium. In this paper, we introduce the First-Shell Hydration (FiSH) model as a first attempt to introduce first-shell effects within a continuum solvation framework. One such effect is charge asymmetry, which is captured by a modified electrostatic term within the FiSH model by introducing a nonlinear correction of atomic Born radii based on the induced surface charge density. A hybrid van der Waals formulation consisting of two continuum zones has been implemented. A shell of water restricted to and uniformly distributed over the solvent-accessible surface (SAS) represents the first solvation shell. A second region starting one solvent diameter away from the SAS is treated as bulk water with a uniform density function. Both the electrostatic and van der Waals terms of the FiSH model have been calibrated against linear interaction energy (LIE) data from molecular dynamics simulations. Extensive testing of the FiSH model was carried out on large hydration data sets including both simple compounds and drug-like molecules. The FiSH model accurately reproduces contributing terms, absolute predictions relative to experimental hydration free energies, and functional class trends of LIE MD simulations. Overall, the implementation of the FiSH model achieves a very acceptable performance and transferability improving over previously developed solvation models, while being complemented by a sound physical foundation.

Entities:  

Year:  2010        PMID: 26615695     DOI: 10.1021/ct9006037

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  17 in total

1.  Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction.

Authors:  Traian Sulea; Hervé Hogues; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2011-12-25       Impact factor: 3.686

2.  Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models.

Authors:  Traian Sulea; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2011-12-22       Impact factor: 3.686

3.  Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

Authors:  Enrico O Purisima; Christopher R Corbeil; Traian Sulea
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

4.  "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.

Authors:  Andrea Bazzoli; John Karanicolas
Journal:  J Comput Chem       Date:  2017-03-20       Impact factor: 3.376

5.  Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

Authors:  Hari S Muddana; C Daniel Varnado; Christopher W Bielawski; Adam R Urbach; Lyle Isaacs; Matthew T Geballe; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2012-02-25       Impact factor: 3.686

6.  Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

Authors:  Jaydeep P Bardhan; Pavel Jungwirth; Lee Makowski
Journal:  J Chem Phys       Date:  2012-09-28       Impact factor: 3.488

7.  Extended solvent-contact model approach to SAMPL4 blind prediction challenge for hydration free energies.

Authors:  Hwangseo Park
Journal:  J Comput Aided Mol Des       Date:  2014-02-20       Impact factor: 3.686

8.  Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge.

Authors:  Hervé Hogues; Traian Sulea; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2014-01-29       Impact factor: 3.686

9.  Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.

Authors:  Jaydeep P Bardhan; Matthew G Knepley
Journal:  J Chem Phys       Date:  2014-10-07       Impact factor: 3.488

10.  Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

Authors:  Lauren Wickstrom; Nanjie Deng; Peng He; Ahmet Mentes; Crystal Nguyen; Michael K Gilson; Tom Kurtzman; Emilio Gallicchio; Ronald M Levy
Journal:  J Mol Recognit       Date:  2015-08-10       Impact factor: 2.137

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