Examining molecular factors of inactive versus active bivalent EGFR inhibitors: A missing link in fragment-based drug design.

The optimization of linkers that connect fragments within drug binding sites represents an impediment in fragment-based drug discovery (FBDD). To improve our understand of the molecular factors that enable effective fragment linking, we have produced a series of compounds that bind to the ATP and allosteric sites of the EGFR kinase domain connected by two distinct linker structures. We find the linker is responsible for opposing impacts on potency against EGFR mutants, the most potent of which are active in human cancer cells. Comparison of X-ray cocrystal structures of active versus inactive molecules provide unique experimentally derived insights into linker design criteria such as how fragment flexibility and intermolecular interactions can serve compound design broadly in drug optimization.