Structure Based Design Synthesis Pharmacophore ModelingVirtual Screening and Molecular Docking Studies for Identificationof Novel Cyclophilin D Inhibitors

摘要

Cyclophilin D (CypD) is a peptidyl prolyl isomerase F that resides in the mitochondrial matrix and associates with the inner mitochondrial membrane during the mitochondrial membrane permeability transition. CypD plays a central role in opening the mitochondrial membrane permeability transition pore (mPTP) leading to cell death and has been linked to Alzheimer’s disease (AD). Because CypD interacts with amyloid beta (Aβ) to exacerbate mitochondrial and neuronal stress, it is a potential target for drugs to treat AD. Since appropriately designed small organic molecules might bind to CypD and block its interaction with Aβ, 20 trial compounds were designed using known procedures that started with fundamental pyrimidine and sulfonamide scaffolds know to have useful therapeutic effects. Two-dimensional (2D) quantitative structure–activity relationship (QSAR) methods were applied to 40 compounds with known IC50 values. These formed a training set and were followed by a trial set of 20 designed compounds. A correlation analysis was carried out comparing the statistics ofthe measured IC50 with predicted values for both sets.Selectivity-determining descriptors were interpreted graphically interms of principle component analyses. These descriptors can be veryuseful for predicting activity enhancement for lead compounds. A 3Dpharmacophore model was also created. Molecular dynamics simulationswere carried out for the 20 trial compounds with known IC50 values, and molecular descriptors were determined by 2D QSAR studiesusing the Lipinski rule-of-five. Fifteen of the 20 molecules satisfiedall 5 Lipinski rules, and the remaining 5 satisfied 4 of the 5 Lipinskicriteria and nearly satisfied the fifth. Our previous use of 2D QSAR,3D pharmacophore models, and molecular docking experiments to successfullypredict activity indicates that this can be a very powerful techniquefor screening large numbers of new compounds as active drug candidates.These studies will hopefully provide a basis for efficiently designingand screening large numbers of more potent and selective inhibitorsfor CypD treatment of AD.