Binding of Inhibitors to BACE1 Affected by pH-Dependent Protonation: An Exploration from Multiple Replica Gaussian Accelerated Molecular Dynamics and MM-GBSA Calculations
- Jianzhong Chen*
Jianzhong Chen*Email: [email protected], [email protected]School of Science, Shandong Jiaotong University, Jinan 250357, ChinaMore by Jianzhong Chen
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- Shaolong Zhang
Shaolong ZhangSchool of Physics and Electronics, Shandong Normal University, Jinan 250358, ChinaMore by Shaolong Zhang
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- Wei Wang
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- Haibo Sun
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- Qinggang Zhang
Qinggang ZhangSchool of Physics and Electronics, Shandong Normal University, Jinan 250358, ChinaMore by Qinggang Zhang
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- Xinguo Liu*
Xinguo Liu*Email: [email protected]School of Physics and Electronics, Shandong Normal University, Jinan 250358, ChinaMore by Xinguo Liu
Abstract
To date, inhibiting the activity of β-amyloid cleaving enzyme 1 (BACE1) has been considered an efficient approach for treating Alzheimer’s disease (AD). In the current work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations and the molecular mechanics general Born surface area (MM-GBSA) method were combined to investigate the effect of pH-dependent protonation on the binding of the inhibitors CS9, C6U, and 6WE to BACE1. Dynamic analyses based on the MR-GaMD trajectory show that pH-dependent protonation strongly affects the structural flexibility, correlated motions, and dynamic behavior of inhibitor-bound BACE1. According to the constructed free energy profiles, in the protonated state at low pH, inhibitor-bound BACE1 tends to populate at more conformations than in high pH. The binding free energies calculated by MM-GBSA suggest that inhibitors possess stronger binding abilities under the protonation conditions at high pH than under the protonation conditions at low pH. Moreover, pH-dependent protonation exerts a significant effect on the hydrogen bonding interactions of CS9, C6U, and 6WE to BACE1, which correspondingly alters the binding abilities of the three inhibitors to BACE1. Furthermore, in different protonated environments, three inhibitors share common interaction clusters and similar binding sites in BACE1, which are reliably used as efficient targets for the design of potent inhibitors of BACE1.
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