Cyclophilins are regarded as potential drug targets for the treatment of several diseases such as AIDS and malaria. In the present study, the binding of a series of Xaa-Pro dipeptide ligands to human cyclophilin A (CypA) or <i>C. elegans</i> cyclophilin 3 (Cyp3) has been studied using enzymatic activity assays and crystal soaking experiments. The binding energies and dissociation constant (<i>K</i><sub>d</sub>) values of the dipeptide ligands are found to be essentially identical in the crystal and in solution. Three Xaa-Pro/Cyp complex crystal structures were determined in order to calculate their <i>K</i><sub>d</sub> values. A set of 9 known CypA-ligand complex structures were used for docking and scoring performance evaluation, which was carried out by our in-house virtual screening suite LIDAEUS. The results indicate that with appropriate parameterisation LIDAEUS is competent in predicting correct poses. Docking and scoring parameters used in screening for novel CypA ligands with LIDAEUS were optimised during the re-docking experiments. A composite <i>S<sub>screening</sub> </i>score which involved the high weighted PIP (Pose Interactions Profiles) score combined with the low weighted energy score enabled us to identify hits for the target protein from a larch chemical database (ZINC database subset 3.2 million compounds). A post-screening filtering was performed by searching for conserved interactions found in tight binding ligands. This enabled us to select 14 compounds for protein-ligand testing. Six novel CypA ligands were identified by PPIase activity assays and isothermal titration calorimetry competition assays (<i>K</i><sub>d </sub>to CypA in a range of 1-120 μM).
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:653190 |
| Date | January 2007 |
| Creators | Kan, Daphne Wei-Chun |
| Publisher | University of Edinburgh |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/1842/15137 |
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