Kinase enzymes switch functionally from one conformational state to another during the cell cycle. Binding a protein kinase into such a conformation can trap the enzyme, either competing with ATP binding or shifting the equilibrium toward an inactive state, thereby inhibiting the kinase activity. Multiple conformations of a protein kinase target offer an opportunity to design small‐molecule inhibitors with distinct but clinically useful profiles. The rationale underlying this strategy is that in different kinase conformations, the size, availability, and topological distribution of the binding pockets are different, molecular recognition of which can help to develop distinct kinase inhibitors. In particular, as toxicity‐related promiscuity and drug‐resistant mutations currently are two major issues in anti‐kinase therapy, targeting kinase multiple conformations is a structure‐based strategy to optimize the selectivity and acquired resistance profiles of kinase inhibitors in the field of protein kinase drug discovery.
This chapter starts with the introduction of recent important advances and challenges in the early‐stage protein kinase drug discovery. In Section 2, the binding pockets and their topological distributions in multiple conformational states of a kinase target are analyzed and classified. Targeting these different conformations to develop kinase inhibitors with potency, selectivity, and acquired resistance profiles is elucidated and exemplified in Sections 3 and 4. Conclusion remarks are given in Section 5.