Conformational Flexibility, Internal Hydrogen Bonding, and Passive Membrane Permeability:  Successful in Silico Prediction of the Relative Permeabilities of Cyclic Peptides

2006 ◽  
Vol 128 (43) ◽  
pp. 14073-14080 ◽  
Author(s):  
Taha Rezai ◽  
Jonathan E. Bock ◽  
Mai V. Zhou ◽  
Chakrapani Kalyanaraman ◽  
R. Scott Lokey ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Membrane Permeability ◽  
In Silico ◽  
Cyclic Peptides ◽  
Conformational Flexibility ◽  
In Silico Prediction ◽  
Relative Permeabilities ◽  
Internal Hydrogen ◽  
Passive Membrane

In Silico Prediction of Membrane Permeability from Calculated Molecular Parameters

2005 ◽  
Vol 48 (3) ◽  
pp. 805-811 ◽  
Author(s):  
Hanne H. F. Refsgaard ◽  
Berith F. Jensen ◽  
Per B. Brockhoff ◽  
Søren B. Padkjær ◽  
Mette Guldbrandt ◽  
...  
Keyword(s):  
Membrane Permeability ◽  
In Silico ◽  
In Silico Prediction ◽  
Molecular Parameters

scholarly journals Physicochemical Determinants of Passive Membrane Permeability:  Role of Solute Hydrogen-Bonding Potential and Volume.

2002 ◽  
Vol 45 (10) ◽  
pp. 2122-2122 ◽  
Author(s):  
Jay T. Goodwin ◽  
Robert A. Conradi ◽  
Norman F. H. Ho ◽  
Philip S. Burton
Keyword(s):  
Hydrogen Bonding ◽  
Membrane Permeability ◽  
Hydrogen Bonding Potential ◽  
Passive Membrane

Toward the elucidation of the mechanism for passive membrane permeability of cyclic peptides

2019 ◽  
Vol 11 (7) ◽  
pp. 637-639 ◽  
Author(s):  
Sereina Riniker
Keyword(s):  
Membrane Permeability ◽  
Cyclic Peptides ◽  
Passive Membrane

Physicochemical Determinants of Passive Membrane Permeability:  Role of Solute Hydrogen-Bonding Potential and Volume

2001 ◽  
Vol 44 (22) ◽  
pp. 3721-3729 ◽  
Author(s):  
Jay T. Goodwin ◽  
Robert A. Conradi ◽  
Norman F. H. Ho ◽  
Philip S. Burton
Keyword(s):  
Hydrogen Bonding ◽  
Membrane Permeability ◽  
Hydrogen Bonding Potential ◽  
Passive Membrane

scholarly journals Passing the Barrier – How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides

2021 ◽  
Vol 75 (6) ◽  
pp. 518-521
Author(s):  
Stephanie M. Linker ◽  
Shuzhe Wang ◽  
Benjamin Ries ◽  
Thomas Stadelmann ◽  
Sereina Riniker
Keyword(s):  
Membrane Permeability ◽  
Protein Interactions ◽  
Cyclic Peptides ◽  
Rational Design ◽  
Cyclic Peptide ◽  
Md Simulations ◽  
Protein Protein Interactions ◽  
Small Molecule Drugs ◽  
Conformational Dynamic ◽  
Passive Membrane

Proteins with large and flat binding sites as well as protein–protein interactions are considered ' undruggable ' with conventional small-molecule drugs. Cyclic peptides have been found to be capable of binding to such targets with high affinity, making this class of compounds an interesting source for possible therapeutics. However, the oftentimes poor passive membrane permeability of cyclic peptides still imposes restrictions on the applicability of cyclic peptide drugs. Here, we describe how computational methods in combination with experimental data can be used to improve our understanding of the structure–permeability relationship. Especially the conformational dynamic and chameleonic nature of cyclic peptides, which we investigate by a combination of MD simulations and kinetic modeling, is important for their ability to permeate passively through the membrane. The insights from such studies may enable the formulation of design principles for the rational design of permeable cyclic peptides.

scholarly journals A Strategy for in Silico Prediction of the Membrane Permeability of Drugs

2018 ◽  
Vol 91 (11) ◽  
pp. 1618-1624 ◽  
Author(s):  
Yu Fujii ◽  
Erina Yoshida ◽  
Toshiyuki Osakai
Keyword(s):  
Membrane Permeability ◽  
In Silico ◽  
In Silico Prediction

Speciation of cultivated temperate and tropical Pleurotus species –an in silico prediction using conserved sequences

2019 ◽  
Vol 28 (1) ◽  
Author(s):  
Anupam Barh ◽  
V P Sharma ◽  
Shwet Kamal ◽  
Mahantesh Shirur ◽  
Sudheer Kumar Annepu ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Prediction ◽  
Conserved Sequences ◽  
Pleurotus Species
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