Tricyclic Antidepressants as Prospective α‑Synucleinopathy Fighters: Evidence of Protein Binding and Antiaggregation Activity

Intrinsically disordered proteins (IDPs) like α-synuclein
are pivotal in neurodegenerative diseases but present formidable challenges
for drug discovery due to their conformational heterogeneity and lack
of defined binding pockets. Here, we report the finding that clinically
approved tricyclic antidepressants imipramine, amitriptyline, and
doxepin bind directly to monomeric α-synuclein and inhibit its
fibrillation, a key process in Parkinson’s pathology. Using
a combination of NMR spectroscopy (WaterLOGSY and chemical shift perturbation,
CSP) and molecular dynamics simulation methods, we elucidate a nonspecific,
multiligand binding mechanism of tricyclic antidepressants predominantly
targeting the C-terminal domain of the protein. The experimental CSP
magnitudes correlate with the inhibitory potency of ligands, with
imipramine emerging as the most potent inhibitor, and agree with the
contact probabilities with different residues from simulations. The
protein–ligand binding is driven by a dynamic combination of
electrostatic attraction of positively charged ligands to anionic
side chains, π-stacking with aromatic residues, and hydrophobic
contacts. Moreover, simulations show that a single ligand molecule
frequently engages in simultaneous salt-bridge and π-stacking
interactions, unlike some previously studied α-synuclein binders.
Our findings position tricyclic antidepressants as promising scaffolds
for targeting α-synuclein and demonstrate the efficiency of
molecular dynamics approaches for the description of interactions
between small drug molecules and IDPs.