Literature DB >> 34302680

In Silico Prediction of Permeability Coefficients.

Ricardo J Ferreira1.   

Abstract

In silico simulations of biological systems are of the significant importance to obtain insights on specific processes that experimental protocols have difficulty to elucidate. More particularly, and to ensure that a given molecule is able to reach its cellular target, the development of computational methods able to quickly estimate the cellular permeabilities for small molecules can become an important tool in the early stages of drug development. Herein, a computational protocol for predicting permeability coefficients, concerning both membranes and proteins, is presented and discussed.
© 2021. Springer Science+Business Media, LLC, part of Springer Nature.

Keywords:  Inhomogeneous solubility-diffusion model; Membranes; Molecular dynamics; Permeability coefficients; Proteins; Python; Resistance to permeation; Umbrella sampling

Year:  2021        PMID: 34302680     DOI: 10.1007/978-1-0716-1468-6_14

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  23 in total

1.  Theory and simulation of ion conduction in the pentameric GLIC channel.

Authors:  Fangqiang Zhu; Gerhard Hummer
Journal:  J Chem Theory Comput       Date:  2012-03-07       Impact factor: 6.006

Review 2.  Molecular simulation of nonfacilitated membrane permeation.

Authors:  Ernest Awoonor-Williams; Christopher N Rowley
Journal:  Biochim Biophys Acta       Date:  2015-12-17

3.  Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.

Authors:  Jérôme Hénin; Emad Tajkhorshid; Klaus Schulten; Christophe Chipot
Journal:  Biophys J       Date:  2007-10-05       Impact factor: 4.033

Review 4.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

5.  Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins.

Authors:  Silvia Acosta-Gutiérrez; Luana Ferrara; Monisha Pathania; Muriel Masi; Jiajun Wang; Igor Bodrenko; Michael Zahn; Mathias Winterhalter; Robert A Stavenger; Jean-Marie Pagès; James H Naismith; Bert van den Berg; Malcolm G P Page; Matteo Ceccarelli
Journal:  ACS Infect Dis       Date:  2018-08-17       Impact factor: 5.084

6.  Insights on the Mechanism of Action of INH-C10 as an Antitubercular Prodrug.

Authors:  Diogo Vila-Viçosa; Bruno L Victor; Jorge Ramos; Diana Machado; Miguel Viveiros; Jacek Switala; Peter C Loewen; Ruben Leitão; Filomena Martins; Miguel Machuqueiro
Journal:  Mol Pharm       Date:  2017-11-13       Impact factor: 4.939

7.  Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes.

Authors:  Jochen S Hub; Fritz K Winkler; Mike Merrick; Bert L de Groot
Journal:  J Am Chem Soc       Date:  2010-09-29       Impact factor: 15.419

8.  Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics.

Authors:  Ricardo J Ferreira; Peter M Kasson
Journal:  ACS Infect Dis       Date:  2019-10-25       Impact factor: 5.084

9.  Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.

Authors:  Christopher T Lee; Jeffrey Comer; Conner Herndon; Nelson Leung; Anna Pavlova; Robert V Swift; Chris Tung; Christopher N Rowley; Rommie E Amaro; Christophe Chipot; Yi Wang; James C Gumbart
Journal:  J Chem Inf Model       Date:  2016-04-14       Impact factor: 4.956

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