ArticleJournal of chemical theory and computation2012
Convergence of Free Energy Profile of Coumarin in Lipid Bilayer.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 114 citations in OpenAlex.
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- Exploring the potential of silymarin-loaded nanovesicles as an effective drug delivery system for cancer therapy: in vivo, in vitro, and in silico experiments.Naunyn-Schmiedeberg's archives of pharmacology · 2024Article
- Permeation of a Homologous Series of NBD-Labeled Fatty Amines through Lipid Bilayers: A Molecular Dynamics Study.Membranes · 2023Article
- Interactions between Rhodamine Dyes and Model Membrane Systems-Insights from Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2022Article
- Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design.Pharmaceuticals (Basel, Switzerland) · 2021Review
- The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2020Review
- Atomistic Molecular Dynamics Simulations of Propofol and Fentanyl in Phosphatidylcholine Lipid Bilayers.ACS omega · 2020Article
- Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning.European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V · 2019Review
- Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane.Scientific reports · 2017Article
- Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle.The Journal of biological chemistry · 2017Article
- Combination of anti-hypertensive drugs: a molecular dynamics simulation study.Journal of molecular modeling · 2017Article
- Partitioning into Colloidal Structures of Fasted State Intestinal Fluid Studied by Molecular Dynamics Simulations.Langmuir : the ACS journal of surfaces and colloids · 2016Article
- Two Relations to Estimate Membrane Permeability Using Milestoning.The journal of physical chemistry. B · 2016Article
- Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.Journal of chemical information and modeling · 2016Article
- Structural perturbation of a dipalmitoylphosphatidylcholine (DPPC) bilayer by warfarin and its bolaamphiphilic analogue: A molecular dynamics study.Journal of colloid and interface science · 2016Article
- Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange.The Journal of membrane biology · 2015Article
- A method to predict blood-brain barrier permeability of drug-like compounds using molecular dynamics simulations.Biophysical journal · 2014Article
- Photouncaging of ceramides promotes reorganization of liquid-ordered domains in supported lipid bilayers.Langmuir : the ACS journal of surfaces and colloids · 2013Article
- Drug permeability prediction using PMF method.Journal of molecular modeling · 2013Article
- Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR?Chemical biology & drug design · 2013Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer normal calculated by biased MD simulations (∼7 μs in total). The convergences in time of free energy profiles calculated by both umbrella sampling and z-constraint techniques are thoroughly analyzed. Two sets of starting structures are also considered, one from unbiased MD simulation and the other from "pulling" coumarin along the bilayer normal. The structures obtained by pulling simulation contain water defects on the lipid bilayer surface, while those acquired from unbiased simulation have no membrane defects. The free energy profiles converge more rapidly when starting frames from unbiased simulations are used. In addition, z-constraint simulation leads to more rapid convergence than umbrella sampling, due to quicker relaxation of membrane defects. Furthermore, we show that the choice of RESP, PRODRG, or Mulliken charges considerably affects the resulting free energy profile of our model drug along the bilayer normal. We recommend using z-constraint biased MD simulations based on starting geometries acquired from unbiased MD simulations for efficient calculation of convergent free energy profiles of druglike molecules along bilayer normals. The calculation of free energy profile should start with an unbiased simulation, though the polar molecules might need a slow pulling afterward. Results obtained with the recommended simulation protocol agree well with available experimental data for two coumarin derivatives.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.