Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations

The RaPID Platform for the Discovery of Pseudo-Natural Macrocyclic Peptides

(2021) Yuki Goto et al.   ACCOUNTS OF CHEMICAL RESEARCH

Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations

(2021) Masatake Sugita et al.   Journal of Chemical Information and Modeling

Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides

(2021) Shuzhe Wang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Cyclosporin Structure and Permeability: From A to Z and Beyond

(2021) Karen M. Corbett et al.   JOURNAL OF MEDICINAL CHEMISTRY

Drug‐like properties in macrocycles above MW 1000: Backbone rigidity vs. side‐chain lipophilicity

(2020) Akihiro Furukawa et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

How cholesterol stiffens unsaturated lipid membranes

(2020) Saptarshi Chakraborty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membrane Permeability in Cyclic Peptides is Modulated by Core Conformations

(2020) Flaviu Cipcigan et al.   Journal of Chemical Information and Modeling

Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations

(2019) Zanxia Cao et al.   JOURNAL OF CHEMICAL PHYSICS

Conformation and Permeability: Cyclic Hexapeptide Diastereomers

(2019) Satoshi Ono et al.   Journal of Chemical Information and Modeling

Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space

(2018) Vasanthanathan Poongavanam et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants

(2018) Rui Sun et al.   JOURNAL OF CHEMICAL PHYSICS

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model

(2018) Oriana De Vos et al.   Journal of Chemical Theory and Computation

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

(2018) Matteo Rossi Sebastiano et al.   JOURNAL OF MEDICINAL CHEMISTRY

Conformational Flexibility Is a Determinant of Permeability for Cyclosporin

(2018) Conan K. Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculating Kinetic Rates and Membrane Permeability from Biased Simulation

(2018) Magd Badaoui et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides

(2018) Jagna Witek et al.   Journal of Chemical Information and Modeling

Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules

(2018) Callum J. Dickson et al.   Journal of Chemical Information and Modeling

Lipophilic Permeability Efficiency Reconciles the Opposing Roles of Lipophilicity in Membrane Permeability and Aqueous Solubility

(2018) Matthew R. Naylor et al.   JOURNAL OF MEDICINAL CHEMISTRY

Nonclassical Size Dependence of Permeation Defines Bounds for Passive Adsorption of Large Drug Molecules

(2017) Cameron R. Pye et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting a Drug’s Membrane Permeability: A Computational Model Validated With in Vitro Permeability Assay Data

(2017) Brian J. Bennion et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Membrane Rigidity Determined by Atomic Force Microscopy Is a Parameter of the Permeability of Liposomal Membranes to the Hydrophilic Compound Calcein

(2016) Yuki Takechi-Haraya et al.   AAPS PHARMSCITECH

Design and Development of a Cyclic Decapeptide Scaffold with Suitable Properties for Bioavailability and Oral Exposure

(2016) Marianne Fouché et al.   ChemMedChem

Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs

(2016) Adrian Whitty et al.   DRUG DISCOVERY TODAY

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition

(2016) Siegfried S. F. Leung et al.   Journal of Chemical Information and Modeling

Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States

(2016) Jagna Witek et al.   Journal of Chemical Information and Modeling

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

(2016) Christopher T. Lee et al.   Journal of Chemical Information and Modeling

Passive Membrane Permeability in Cyclic Peptomer Scaffolds Is Robust to Extensive Variation in Side Chain Functionality and Backbone Geometry

(2016) Akihiro Furukawa et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

(2016) Callum J. Dickson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations

(2014) Timothy S. Carpenter et al.   BIOPHYSICAL JOURNAL

Oral Druggable Space beyond the Rule of 5: Insights from Drugs and Clinical Candidates

(2014) Bradley Croy Doak et al.   CHEMISTRY & BIOLOGY

Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

(2013) Florian Zocher et al.   BIOPHYSICAL JOURNAL

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal

(2013) Chris Neale et al.   Journal of Chemical Theory and Computation

Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers

(2013) Joakim P. M. Jämbeck et al.   Journal of Physical Chemistry Letters

Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes

(2012) Christian L. Wennberg et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion

(2012) Giulia Parisio et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers

(2011) Chris Neale et al.   Journal of Chemical Theory and Computation

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY