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Bioinformatics Advance Access originally published online on September 5, 2007
Bioinformatics 2007 23(20):2678-2685; doi:10.1093/bioinformatics/btm431
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Structure-based calculation of drug efficiency indices

Csaba Hetényi 1,2,*, Uko Maran 1, Alfonso T. García-Sosa 1 and Mati Karelson 1

1Institute of Chemical Physics, University of Tartu, 2 Jakobi Street, 51014 Tartu, Estonia and 2Department of Organic Chemistry, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary

*To whom correspondence should be addressed.


  Abstract

Motivation: The efficiency indices (EI's) have been derived from the experimental binding affinities of drug candidates to macromolecules. These ‘two-in-one’ measures include information on both pharmacodynamics and pharmacokinetics of the candidate molecules. The time-consuming experimental measurement of binding affinities of extensive molecule libraries may become a bottle-neck of large scale generation and application of EI's.

Results: To overcome this limitation, structure-based calculation of new EI's is introduced using the modified free energy function of the popular program package AutoDock. The results are validated on experimental binding data of biochemical systems such as potent inhibitors bound to ß-secretase, a key enzyme of Alzheimer's disease and various drug–protein complexes. Application of new EI's is tested. Thermodynamics of EI's and their role in virtual high - throughput screening of drugs and in the development of docking programs are discussed.

Contact: csabahete{at}yahoo.com

Supplementary information: Accompanies this manuscript on the publisher's web site.

Associate Editor: Anna Tramontano

Received on March 17, 2007; revised on August 6, 2007; accepted on August 18, 2007

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