Predicting Inactive Conformations Of Protein Kinases

Protein kinases are important drug targets. The conserved motif Asp-Phe-Gly (DFG) in kinase domains has been found to possess two characteristic conformations and correspond to different activation states of kinases:the active DFG-in conformation and the inactive DFG-out conformation. Recently, it is very interesting to develop type-II inhibitors which target the DFG-out conformation and are more specific than type-I inhibitors binding to the active DFG-in conformation.Solving crystal structures of kinases with the DFG-out conformation remains a challenge. And this seriously hampers the application of the structure-based approaches in development of novel type-Ⅱ inhibitors. To overcome this limitation, this study presents a computational approach for predicting the DFG-out inactive conformation using the DFG-in active structures, and develop related conformational selection protocols for the uses of the predicted DFG-out models in the binding pose prediction and virtual screening of type-Ⅱ ligands. With the DFG-out models, we predicted the binding poses for known type-Ⅱ inhibitors, and the results were found in good agreement with the X-ray crystal structures. We also tested the abilities of the DFG-out models to recognize their specific type-Ⅱ inhibitors by screening a database of small molecules. The AUC (area under curve) results indicated that the predicted DFG-out models were selective toward their specific type-Ⅱ inhibitors. Therefore, the computational approach and protocols presented here are very promising for the structure-based design and screening of novel type-Ⅱ kinase inhibitors.To predict the capability of different kinases to adopt the DFG-out conformation, we used structure-based models (SBM) to simulate DFG flips of kinases ABL1and LCK, and flip trajectories from the DFG-in to DFG-out conformations were obtained. We employed local-conformational sampling method to sample the conformational space of the intermediate states and calculated potential of mean force along the pathway. Results demonstrated that ABL1adopts the DFG-out conformation more easily than LCK. This is consistent with the observation from crystallization experiments of these two kinases. Therefore, the SBM method is a promising approach for efficient simulation of DFG flips. If combining with our method to predict inactive conformations, the SBM method could be used to elucidate the capability of various kinases to adopt the DFG-out conformation, and provide useful information for discovery of novel type-Ⅱ inhibitors targeting the given kinases.