Literature DB >> 31939104

A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approach.

Evrim Arslan1, Basak K Findik1, Viktorya Aviyente2.   

Abstract

In this study quantum mechanical methods were used to predict the solvation energies of a series of drug-like molecules both in water and in octanol, in the context of the SAMPL6 n-octanol/water partition coefficient challenge. In pharmaceutical design, n-octanol/water partition coefficient, LogP, describes the drug's hydrophobicity and membrane permeability, thus, a well-established theoretical method that rapidly determines the hydrophobicity of a drug, enables the progress of the drug design. In this study, the solvation free energies were obtained via six different methodologies (B3LYP, M06-2X and ωB97XD functionals with 6-311+G** and 6-31G* basis sets) by taking into account the environment implicitly; the methodology chosen (B3LYP/6-311+G**) was used later to evaluate ΔGsolv by using explicit water as solvent. We optimized each conformer in different solvents separately, our calculations have shown that the stability of the conformers is highly dependent on the solvent environment. We have compared implicitly and explicitly solvated systems, the interaction of one explicit water with drug-molecules at the proper location leads to the prediction of more accurate LogP values.

Entities:  

Keywords:  Computer-aided drug design; DFT; Octanol/water partition coefficient; SAMPL6; Solvation free energies

Mesh:

Substances:

Year:  2020        PMID: 31939104     DOI: 10.1007/s10822-020-00284-3

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  25 in total

1.  Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules.

Authors:  Yu Takano; K N Houk
Journal:  J Chem Theory Comput       Date:  2005-01       Impact factor: 6.006

2.  Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields.

Authors:  Hari S Muddana; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2012-01-25       Impact factor: 3.686

3.  Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

Authors:  Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2009-05-07       Impact factor: 2.991

4.  Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections.

Authors:  Jeng-Da Chai; Martin Head-Gordon
Journal:  Phys Chem Chem Phys       Date:  2008-09-29       Impact factor: 3.676

5.  Using molecular simulation to predict solute solvation and partition coefficients in solvents of different polarity.

Authors:  Nuno M Garrido; Miguel Jorge; António J Queimada; Eugénia A Macedo; Ioannis G Economou
Journal:  Phys Chem Chem Phys       Date:  2011-04-12       Impact factor: 3.676

6.  Reversed phase HPLC with high temperature ethanol/water mobile phases as a green alternative method for the estimation of octanol/water partition coefficients.

Authors:  Phillip B Ogden; John G Dorsey
Journal:  J Chromatogr A       Date:  2019-05-03       Impact factor: 4.759

7.  The influence of hydrogen bonding on partition coefficients.

Authors:  Nádia Melo Borges; Peter W Kenny; Carlos A Montanari; Igor M Prokopczyk; Jean F R Ribeiro; Josmar R Rocha; Geraldo Rodrigues Sartori
Journal:  J Comput Aided Mol Des       Date:  2017-01-04       Impact factor: 3.686

8.  SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model.

Authors:  Caitlin C Bannan; David L Mobley; A Geoffrey Skillman
Journal:  J Comput Aided Mol Des       Date:  2018-10-15       Impact factor: 3.686

9.  Measuring log Kow coefficients of neutral species of perfluoroalkyl carboxylic acids using reversed-phase high-performance liquid chromatography.

Authors:  Qian Xiang; Guoqiang Shan; Wei Wu; Hangbiao Jin; Lingyan Zhu
Journal:  Environ Pollut       Date:  2018-08-08       Impact factor: 8.071

Review 10.  The SAMPL4 host-guest blind prediction challenge: an overview.

Authors:  Hari S Muddana; Andrew T Fenley; David L Mobley; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2014-03-06       Impact factor: 3.686

View more
  3 in total

1.  Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge.

Authors:  Mehtap Işık; Teresa Danielle Bergazin; Thomas Fox; Andrea Rizzi; John D Chodera; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2020-02-27       Impact factor: 3.686

2.  SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules.

Authors:  Basak Koca Fındık; Zeynep Pinar Haslak; Evrim Arslan; Viktorya Aviyente
Journal:  J Comput Aided Mol Des       Date:  2021-06-24       Impact factor: 3.686

Review 3.  Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects.

Authors:  Rossella Migliore; Tarita Biver; Giampaolo Barone; Carmelo Sgarlata
Journal:  Biomolecules       Date:  2022-03-07
  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.