TIde: a software for the systematic scanning of drug targets in kinetic network models.
BACKGROUND
During the stages of the development of a potent drug candidate compounds can fail for several reasons. One of them, the efficacy of a candidate, can be estimated in silico if an appropriate ordinary differential equation model of the affected pathway is available. With such a model at hand it is also possible to detect reactions having a large effect on a certain variable such as a substance concentration.


RESULTS
We show an algorithm that systematically tests the influence of activators and inhibitors of different type and strength acting at different positions in the network. The effect on a quantity to be selected (e.g. a steady state flux or concentration) is calculated. Moreover, combinations of two inhibitors or one inhibitor and one activator targeting different network positions are analysed. Furthermore, we present TIde (Target Identification), an open source, platform independent tool to investigate ordinary differential equation models in the common systems biology markup language format. It automatically assigns the respectively altered kinetics to the inhibited or activated reactions, performs the necessary calculations, and provides a graphical output of the analysis results. For illustration, TIde is used to detect optimal inhibitor positions in simple branched networks, a signalling pathway, and a well studied model of glycolysis in Trypanosoma brucei.


CONCLUSIONS
Using TIde, we show in the branched models under which conditions inhibitions in a certain pathway can affect a molecule concentrations in a different. In the signalling pathway we illuminate which inhibitions have an effect on the signalling characteristics of the last active kinase. Finally, we compare our set of best targets in the glycolysis model with a similar analysis showing the applicability of our tool.
Schulz
Marvin
M
Theoretical Biophysics, Institute for Biology, Humboldt Universität zu Berlin, Invadilenstrasse, 42, 10115 Berlin, Germany. marvin.schulz@biologie.hu-berlin.de
Bakker
Barbara M
BM
Klipp
Edda
E
D019295:Computational Biology / Q000379:methods*; D006019:Glycolysis; D007700:Kinetics; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014346:Trypanosoma brucei brucei / Q000378:metabolism