Inhibitor fluorination pattern modulates protein surface dynamics and chemically induced dimerization

Chemically induced proximity is a powerful strategy to regulate cellular processes using small-molecule ligands that act as "molecular glues" to influence the lifetime, localization, and function of biological targets. However, the structure-activity relationships governing such inducible interactions remain elusive. Here, using a series of self-assembling homodimerizers that target an essential parasitic redox enzyme, we present a systematic, fluorination-guided strategy to tune induced protein homodimer affinity by two orders of magnitude. Combining NMR spectroscopy, MD simulations, chromatography, multi-angle light scattering, mass spectrometry, calorimetry, and functional assays, we demonstrate that the fluorination pattern of the dimerizer tunes homodimer affinity by modulating the conformational dynamics of both the bound ligand and the protein residues constituting the dimer interface. These findings establish a generalizable framework for understanding how ligand fluorination shapes protein surface dynamics and induced protein interactions. They further reveal how the fluorination pattern of molecular glues modulates protein assembly across biologically relevant affinity ranges, providing mechanistic principles for the rational design of proximity-inducing molecules.