Structural insight into G2019S mutated LRRK2 kinase and brain-penetrant type I inhibitor complex: a molecular dynamics approach

Abstract

More than 40 mutations in the multidomain leucine-rich repeat kinase 2 (LRRK2) are found and mutation G2019S in the kinase domain is the most concerned with Parkinson’s disease (PD). The discovery of the various types of inhibitors has largely emerged recently. However, the comparative study on molecular insight in WT and G2019S LRRK2 kinase domain upon binding of the inhibitors has not yet been explored in detail. This work considered five ATP-competitive Type I inhibitors complexed with WT and mutated LRRK2 kinase. Three reported potent and brain-penetrant inhibitors, GNE-7915, PF-06447475 and MLi-2 (comp1, comp2 and comp3 respectively) and also, another two inhibitors, Pyrrolo[2,3-b] pyridine derivative (comp4) and Pyrrolo[2,3-d] pyrimidine derivative (comp5), were used. In this work, classical and accelerated molecular dynamics (cMD and aMD) simulations were performed for a total of 12 systems (apo and holo). This study found structural and thermodynamic stability for all the inhibitors. Comparatively larger molecules (size 15.3 − 15.4 Å), comp1, comp3 and comp5, showed more selectivity towards mutated LRRK2 kinase in terms of flexibility of residues, compactness and dynamics of kinase, the stability inside the binding-pocket. Also, inhibitors comp3 and comp5 showed higher binding affinity towards G2019S LRRK2 among the five. Residues, E1948 and A1950 (in hinge region) were observed mainly to form hydrogen bonds with inhibitors. Finally, MLi-2 showed a conformational rearrangement by dihedral flipping in both WT and mutated systems but got stability in G2019S LRRK2. This work could potentially help design more improved and effective Type I inhibitors for G2019S LRRK2 kinase.

Among five Type-I inhibitor molecules, comp1 (GNE-7915), comp2 (PF-06447475), comp3 (MLi-2), comp4 (Pyrrolo[2,3-b]pyridine derivative), comp5 (Pyrrolo[2,3-d]pyrimidine derivative), comparatively larger molecules (comp1, comp3 and comp5) showed selectivity towards G2019S LRRK2 and a stable conformation for MLi-2 (after dihedral flipping of the molecule) was found in the mutated system.

Communicated by Ramaswamy H. Sarma

Keywords:

• Molecular dynamics
• LRRK2 kinase domain
• CHK1 kinase
• dynamic cross-correlation
• inhibitor

Acknowledgement

The support and the resources provided by PARAM Shivay Facility under the National Supercomputing Mission, Government of India at the Indian Institute of Technology, Varanasi is gratefully acknowledged.

Author contributions

A.N. and N. P. designed the research problem. A. N. and R.K.R. prepared systems and performed simulations. A.N. and K.K.B. did the analyses and wrote the manuscript.

Disclosure statement

The authors declare no competing financial interest.

Additional information

Funding

N.P. acknowledges CRG/2020/002308 for funding.