Capturing Differences in the Regulation of LRRK2 Dynamics and Conformational States by Small Molecule Kinase Inhibitors

by Selleckchem | Oct 14 2023

Mutations in the human leucine rich repeat protein kinase-2 (LRRK2) create risk factors for Parkinson's disease, and pathological functions of LRRK2 are often correlated with aberrant kinase activity. Past research has focused on developing selective LRRK2 kinase inhibitors. In this study, we combined enhanced sampling simulations with HDX-MS to characterize the inhibitor-induced dynamic changes and the allosteric communications within the C-terminal domains of LRRK2, LRRK2RCKW. We find that the binding of MLi-2 (a type I kinase inhibitor) stabilizes a closed kinase conformation and reduces the global dynamics of LRRK2RCKW, leading to a more compact LRRK2RCKW structure. In contrast, the binding of Rebastinib (a type II kinase inhibitor) stabilizes an open kinase conformation, which promotes a more extended LRRK2RCKW structure. By probing the distinct effects of the type I and type II inhibitors, key interdomain interactions are found to regulate the communication between the kinase domain and the GTPase domain. The intermediate states revealed in our simulations facilitate the efforts toward in silico design of allosteric modulators that control LRRK2 conformations and potentially mediate the oligomeric states of LRRK2 and its interactions with other proteins.

Comments:

The research study you described combines enhanced sampling simulations with hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the effects of kinase inhibitors on the dynamic behavior and allosteric communications within the C-terminal domains of the human leucine-rich repeat protein kinase-2 (LRRK2), specifically LRRK2RCKW. Mutations in LRRK2 are associated with an increased risk of Parkinson's disease, and aberrant kinase activity is implicated in the pathological functions of LRRK2.

The study focused on two types of kinase inhibitors: MLi-2, a type I inhibitor, and Rebastinib, a type II inhibitor. The researchers aimed to characterize the conformational changes induced by these inhibitors and understand their impact on the dynamics of LRRK2RCKW.

The findings of the study reveal that binding of MLi-2 stabilizes a closed conformation of the kinase domain and reduces the overall dynamics of LRRK2RCKW. This leads to a more compact structure of LRRK2RCKW. In contrast, the binding of Rebastinib stabilizes an open conformation of the kinase domain, promoting a more extended structure of LRRK2RCKW.

By investigating the distinct effects of type I and type II inhibitors, the study identified key interdomain interactions that regulate the communication between the kinase domain and the GTPase domain of LRRK2. These interdomain interactions play a crucial role in mediating the conformational changes induced by the inhibitors.

The intermediate states revealed by the simulations provide insights that can aid in the development of in silico design strategies for allosteric modulators. Such modulators have the potential to control the conformational states of LRRK2, regulate its oligomeric states, and modulate its interactions with other proteins. This knowledge could contribute to the development of novel therapeutic approaches for Parkinson's disease by targeting LRRK2 and its aberrant kinase activity.