Linker Modification Enables Control of Key Functional Group Orientation in Macrocycles

Macrocycles are promising drug modalities that can enable unique ways of conformational preorganization, but how even minor modifications to a macrocyclic scaffold influence the conformational preorganization remains poorly understood. Here, we show how macrocyclization and further derivatization of the linker region can improve affinity, selectivity, and plasma stability in a highly atom-efficient manner. A single, solvent-exposed methyl group was found to improve binding affinity up to 10× over the nonmethylated analog. This led to highly ligand-efficient macrocycles with good brain permeability, improved solubility, and a promising in vivo profile for the FK506-binding protein 51 (FKBP51), a key regulator of the human stress response. Using high-resolution cocrystal structures and molecular dynamics simulations, we found that small linker variations can be tuned to shift the orientation of a key carbonyl group into an advantageous position. This effect is specific to macrocycles, highlighting their potential for fine-tuned adjustments to enable desired properties.