BackgroundThe most common mutation in the Leucine-rich repeat kinase 2 gene (LRRK2), G2019S, causes familial Parkinson’s Disease (PD) and renders the encoded protein kinase hyperactive. To date, the molecular effects of chronic LRRK2 inhibition have not yet been examined in vivo. MethodsWe evaluated the utility of newly available phospho-antibodies for Rab substrates pT73 Rab10, pS106 Rab12, pT71 Rab29 and LRRK2 autophosphorylation to examine the pharmacodynamic response to acute treatment paradigms with the potent and specific LRRK2 inhibitor, MLi-2, in brain and peripheral tissue in G2019S LRRK2 knock-in mice to define the relative target engagement between brain and LRRK2-enriched peripheral tissues. The molecular effects of 10 days and 10 weeks of chronic in-diet dosing were also evaluated using TMTpro reagents for LC-MS/MS total and phospho- proteomics in brain and kidney tissues. ResultsWe report higher sensitivity of LRRK2 autophosphorylation to MLi-2 treatment and slower recovery in washout conditions compared to Rab GTPases phosphorylation, and we identify pS106 Rab12 as a robust readout of downstream LRRK2 activity across tissues. The downstream effects of long-term chronic LRRK2 inhibition in vivo were evaluated in G2019S LRRK2 knock-in mice by phospho- and total proteomic analyses following an in-diet administration of MLi-2 for 10 weeks. We observed alterations in endolysosomal and trafficking pathways in the kidney that were sensitive to MLi-2 treatment and that we validated biochemically. Furthermore, a subtle but distinct biochemical signature affecting mitochondrial proteins was observed in brain tissue in the same animals that was reverted by kinase inhibition. ConclusionsThis is the first study to examine the molecular underpinnings of chronic LRRK2 inhibition in a preclinical in vivo PD model and highlights cellular processes that may be influenced by therapeutic strategies aimed at restoring LRRK2 physiological activity in PD patients.