- Poster presentation
- Open Access
Selectivity of new caspase 3 and 8 tetrapeptide substrates can be explained by automated docking analysis
© Schulz et al; licensee BioMed Central Ltd. 2009
- Published: 05 June 2009
- Apoptotic Cell Death
- Cysteine Protease
- Docking Result
- Detect Cell Death
Caspases are cysteine proteases and are considered key-mediators in apoptotic cell death. Selective quantification of the various caspase activities in cancer cells is important for detecting cell death caused by cancer therapy. We have designed and synthesized a series of novel fluorogenic tetrapeptide substrates for caspase 8 and investigated the substrates for selective cleavage by either caspases 3 or 8 in enzyme assays. At the same time we have used the automated docking program AutoDock (ver 3, [1, 2]) to dock the new substrates into the active sites of X-ray crystal structures of human caspases 3 and 8, respectively. AutoDock was confirmed to be an appropriate tool for substrate binding prediction because substrate docking results are comparable with documented X-ray crystal structure of caspase 3 and 8 bounded with analogous tetrapeptide inhibitors [3, 4]. Enzyme-substrate conformations with changes in free energy of binding (ΔG) were calculated with AutoDock and compared to the experimental determined Michaelis-Menten constant Km. A significant correlation between the experimental Km and theoretical ΔG was found. Enzyme kinetics showed the substrates to have 100-fold lower Km-values for caspase 8 compared to caspase 3. This selectivity was reflected in the significantly larger negative ΔG-values between the substrates docked to caspase 8 as opposed to caspase 3. These results will help in the design of even more selective caspase substrates.
- Morris GM, et al: Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. J Comp Chem. 1998, 19: 1639-1662. 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B.View ArticleGoogle Scholar
- Goodsell DS, et al: Automated Docking of Flexible Ligands:Applications of AutoDock. J Mol Recognition. 1996, 9: 1-5. 10.1002/(SICI)1099-1352(199601)9:1<1::AID-JMR241>3.0.CO;2-6.View ArticleGoogle Scholar
- Becker JW, et al: Reducing the Peptidyl Features of Caspase-3 Inhibitors: A Structural Analysis. J Med Chem. 2004, 47: 2466-2474. 10.1021/jm0305523.View ArticleGoogle Scholar
- Watt W, et al: The atomic-resolution structure of human caspase-8, a key activator of apoptosis. Structure Fold Des. 1999, 7: 1135-1143. 10.1016/S0969-2126(99)80180-4.View ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd.