Conservation and divergence in the allosteric architectures of five human protein kinases

Abstract

Protein kinases are central to biological regulation, dysregulated in many diseases, and the targets of a hundred clinically-approved drugs. Structural conservation of kinase active sites makes the development of specific inhibitors challenging. Targeting functional secondary sites can increase specificity, reduce toxicity, overcome resistance mutations, and also activate kinases. However, the functional secondary sites to target in most kinases are unknown, and the conservation of allosteric networks in kinases and other proteins that share the same structural fold is unclear. Here, we quantify the activity and abundance of >160,000 variants to construct complete maps of the energetic and allosteric architectures of five human kinase domains: SRC, FGR, JNK2/MAPK9, ZAK/MAP3K20, and TSSK2. For inhibition, all five kinases have distance-dependent but anisotropic allostery and each kinase has a unique allosteric architecture, surface, and set of pockets to therapeutically target. A set of functional secondary sites is conserved in all five proteins, but other allosteric pockets are protein-specific or switch from inhibitory to activating in different proteins. The differences in the energetic architectures are particularly striking for activation, where the allosteric maps are highly diverged. The allosteric architecture of each kinase is therefore unique, with a distinct set of functional secondary sites to regulate and therapeutically target.