Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study
Abstract
:1. Introduction
2. Results and Discussion
2.1. Inhibition by AHA (1)
2.2. Inhibition by HU (2 and 2′)
2.2.1. Binding Mode 2
2.2.2. Binding Mode 2′
2.3. Inhibition by NBPTO (3)
3. Methods
3.1. Model Preparation and Classical MD Simulations
3.2. QM/MM MD Simulations
3.3. QM-Only Cluster Model Approach
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
References
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Suenaga, S.; Takano, Y.; Saito, T. Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study. Molecules 2023, 28, 2697. https://doi.org/10.3390/molecules28062697
Suenaga S, Takano Y, Saito T. Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study. Molecules. 2023; 28(6):2697. https://doi.org/10.3390/molecules28062697
Chicago/Turabian StyleSuenaga, Shunya, Yu Takano, and Toru Saito. 2023. "Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study" Molecules 28, no. 6: 2697. https://doi.org/10.3390/molecules28062697