Literature DB >> 19115279

In silico prediction of drug solubility: 4. Will simple potentials suffice?

Kai Lüder1, Lennart Lindfors, Jan Westergren, Sture Nordholm, Rasmus Persson, Mikaela Pedersen.   

Abstract

In view of the extreme importance of reliable computational prediction of aqueous drug solubility, we have established a Monte Carlo simulation procedure which appears, in principle, to yield reliable solubilities even for complex drug molecules. A theory based on judicious application of linear response and mean field approximations has been found to reproduce the computationally demanding free energy determinations by simulation while at the same time offering mechanistic insight. The focus here is on the suitability of the model of both drug and solvent, i.e., the force fields. The optimized potentials for liquid simulations all atom (OPLS-AA) force field, either intact or combined with partial charges determined either by semiempirical AM1/CM1A calculations or taken from the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field has been used. The results illustrate the crucial role of the force field in determining drug solubilities. The errors in interaction energies obtained by the simple force fields tested here are still found to be too large for our purpose but if a component of this error is systematic and readily removed by empirical adjustment the results are significantly improved. In fact, consistent use of the OPLS-AA Lennard-Jones force field parameters with partial charges from the COMPASS force field will in this way produce good predictions of amorphous drug solubility within 1 day on a standard desktop PC. This is shown here by the results of extensive new simulations for a total of 47 drug molecules which were also improved by increasing the water box in the hydration simulations from 500 to 2000 water molecules. Copyright 2008 Wiley Periodicals, Inc.

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Year:  2009        PMID: 19115279     DOI: 10.1002/jcc.21173

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  7 in total

1.  Exploratory analysis of kinetic solubility measurements of a small molecule library.

Authors:  Rajarshi Guha; Thomas S Dexheimer; Aimee N Kestranek; Ajit Jadhav; Andrew M Chervenak; Michael G Ford; Anton Simeonov; Gregory P Roth; Craig J Thomas
Journal:  Bioorg Med Chem       Date:  2011-05-13       Impact factor: 3.641

2.  Uniting cheminformatics and chemical theory to predict the intrinsic aqueous solubility of crystalline druglike molecules.

Authors:  James L McDonagh; Neetika Nath; Luna De Ferrari; Tanja van Mourik; John B O Mitchell
Journal:  J Chem Inf Model       Date:  2014-03-11       Impact factor: 4.956

3.  Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening.

Authors:  Sivaraman Dandapani; Gerard Rosse; Noel Southall; Joseph M Salvino; Craig J Thomas
Journal:  Curr Protoc Chem Biol       Date:  2012-09-01

4.  Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Authors:  Guilherme Duarte Ramos Matos; Daisy Y Kyu; Hannes H Loeffler; John D Chodera; Michael R Shirts; David L Mobley
Journal:  J Chem Eng Data       Date:  2017-04-24       Impact factor: 2.694

5.  The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.

Authors:  Michael J Schnieders; Jonas Baltrusaitis; Yue Shi; Gaurav Chattree; Lianqing Zheng; Wei Yang; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2012-04-13       Impact factor: 6.006

Review 6.  Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery.

Authors:  Alex Bunker; Tomasz Róg
Journal:  Front Mol Biosci       Date:  2020-11-25

7.  Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules.

Authors:  Guilherme Duarte Ramos Matos; David L Mobley
Journal:  F1000Res       Date:  2018-05-31
  7 in total

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