Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels

Pan, Yiou; Qi, Renrui; Li, Minghao; Wang, Bingda; Huang, Honglan; Han, Wei

doi:10.1039/d0ra07796h

Cited by 2 publications

(1 citation statement)

References 41 publications

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“…Here, in all the PMF plots (Figures –), the difference in binding energy was observed between paths for the same kinase-inhibitor system as the potential of mean force (PMF) depends on the choice of the collective variable used to describe the reaction pathway. Similar observations have been made by Pan et al and Niu et al…”

Section: Resultsmentioning

confidence: 99%

Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinson’s Disease

Naskar,

Roy,

Srivastava

et al. 2024

J. Phys. Chem. B

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Leucine-rich repeat kinase 2 (LRRK2) remains a viable target for drug development since the discovery of the association of its mutations with Parkinson’s disease (PD). G2019S (in the kinase domain) is the most common mutation for LRRK2-based PD. Though various types of inhibitors have been developed for the kinase domain to reduce the effect of the mutation, understanding the working of these inhibitors at the molecular level is still ongoing. This study focused on the exploration of the dissociation mechanism (pathways) of inhibitors from (WT and G2019S) LRRK2 kinase (using homology model CHK1 kinase), which is one of the crucial aspects in drug discovery. Here, two ATP-competitive type I inhibitors, PF-06447475 and MLi-2 (Comp1 and Comp2 ), and one non-ATP-competitive type II inhibitor, rebastinib (Comp3), were considered for this investigation. To study the unbinding process, random accelerated molecular dynamics simulations were performed. The binding free energies of the three inhibitors for different egression paths were determined using umbrella sampling. This work found four major egression pathways that were adopted by the inhibitors Comp1 (path1, path2, and path3), Comp2 (path1, path2 and path3), and Comp3 (path3 and path4). Also, the mechanism of unbinding for each path and key residues involved in unbinding were explored. Mutation was not observed to impact the preference of the particular egression pathways for both LRRK2-Comp1 and -Comp2 systems. However, the findings suggested that the size of the inhibitor molecules might have an effect on the preference of the egression pathways. The binding energy and residence time of the inhibitors followed a similar trend to experimental observations. The findings of this work might provide insight into designing more potent inhibitors for the G2019S LRRK2 kinase.

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Section: Resultsmentioning

confidence: 99%

Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinson’s Disease

Naskar,

Roy,

Srivastava

et al. 2024

J. Phys. Chem. B

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Investigation of Halide Ion Release Tunnels of Haloalcohol Dehalogenase from Agrobacterium Radiobacter AD1; Computational Study

Belachew

Laxia

2022

Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering

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Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels

Abstract: Adenosine deaminase (ADA), an important enzyme related to purine nucleoside metabolism, can be divided into open conformation and closed conformation according to the inhibitors of binding.

Cited by 2 publications

References 41 publications

Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinson’s Disease

Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinson’s Disease

Investigation of Halide Ion Release Tunnels of Haloalcohol Dehalogenase from Agrobacterium Radiobacter AD1; Computational Study

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