Well-Tempered Metadynamics Simulations Combined with Free Energy Landscape Analysis Uncover the Conformational Transition Pathway of the DYG Motif in LRRK2

Leucine-rich repeat kinase 2 (LRRK2) is one of the most promising targets for the treatment of Parkinson’s Disease. The activation of LRRK2 is regulated by the conserved Asp-Tyr-Gly (DYG) motif of the activation loop. Understanding the flipping process of the DYG motif from active to inactive is crucial for the regulation of LRRK2 kinase catalytic activity. Typically, type I inhibitors stabilize LRRK2 in the active conformation, while type II inhibitors favor the inactive state. To investigate the DYG-flipping mechanism, we performed well-tempered metadynamics simulations on LRRK2 in three distinct states: (1) the apo (ligand-free) state, (2) the type I inhibitor-bound state (DNL201), and (3) the type II inhibitor-bound state (rebastinib). The two-dimensional free energy landscape of DYG flipping in LRRK2 revealed transition pathways between the active (“DYG-in”) and inactive (“DYG-out”) states. Two distinct pathways were identified, which were differentiated by the orientation of Y2018. In the apo system, the DYG motif undergoes an upward flipping motion. Notably, type I inhibitor DNL201 stabilizes LRRK2 in the DYG-in active conformation, whereas type II inhibitor rebastinib promotes a downward flip into the DYG-out inactive state. These findings elucidate the conformational dynamics of LRRK2 in both unbound and ligand-regulated states as well as the mechanistic details of DYG motif flipping. Our study provides critical structural insights for targeted inhibition of LRRK2 kinase activity.