BACK TO CONTENTS   |    PDF   |    NEXT

Title

 

 

 

 

On the hydrophobicity of peptides: Comparing empirical predictions of peptide log P values

Authors

Sarah J. Thompson1,2, Channa K. Hattotuwagama1, John D. Holliday 2 and Darren R. Flower 1*
 

Affiliation

1 Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK; 2 Dept. of Information Studies, University of Sheffield

 

Email

darren.flower@jenner.ac.uk; *Corresponding author

 

Phone

+44 1635 577954

 

Fax

+44 1635 577908

 

Article Type

Prediction Model

 

Date

received October 14, 2006; accepted November 02, 2006; published online November 14, 2006

 

Abstract

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient logP, is useful for the development of predictive Quantitative Structure-Activity Relationships (QSARs). We have investigated the accuracy of available programs for the prediction of logP values for peptides with known experimental values obtained from the literature. Eight prediction programs were tested, of which seven programs were fragment-based methods: XLogP, LogKow, PLogP, ACDLogP, AlogP, Interactive Analysis’s LogP and MlogP; and one program used a whole molecule approach: QikProp. The predictive accuracy of the programs was assessed using r2 values, with ALogP being the most effective (r2 = 0.822) and MLogP the least (r2 = 0.090). We also examined three distinct types of peptide structure: blocked, unblocked, and cyclic. For each study (all peptides, blocked, unblocked and cyclic peptides) the performance of programs rated from best to worse is as follows: all peptides – ALogP, QikProp, PLogP, XLogP, IALogP, LogKow, ACDLogP, and MlogP; blocked peptides – PLogP, XLogP, ACDLogP, IALogP, LogKow, QikProp, ALogP, and MLogP; unblocked peptides – QikProp, IALogP, ALogP, ACDLogP, MLogP, XLogP, LogKow and PLogP; cyclic peptides – LogKow, ALogP, XLogP, MLogP, QikProp, ACDLogP, IALogP. In summary, all programs gave better predictions for blocked peptides, while, in general, logP values for cyclic peptides were under-predicted and those of unblocked peptides were over-predicted.

 

Keywords

 

partition coefficient; logP; peptides; octanol; biphasic system; QSAR  

Citation

Thompson et al., Bioinformation 1(7): 237-241 (2006)
 

Edited by

P. Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

Copyright

Publisher

 

Copyright Transfer Statement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.