A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
Abstract
:1. Introduction
2. Results and Discussion
2.1. Homology Modeling
2.2. Automated Docking
2.3. Molecular Dynamics
2.4. Binding Free Energy
3. Computational Methods
3.1. Homology Modeling and Docking
3.2. Molecular Dynamics Simulation
3.3. Free Energy Calculation
4. Conclusions
Acknowledgements
References
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Name | Compounds | Ki (μM) | ΔGexp |
---|---|---|---|
Bz1 | 68.3 | −5.676 | |
Bz2 | 98.1 | −5.461 | |
Bz3 | 64.7 | −5.708 | |
Bz4 | 29.0 | −6.183 | |
Bz5 | 141.0 | −5.247 | |
Bz6 | 165.0 | −5.154 | |
Bz7 | 190.0 | −5.070 | |
Bz8 | 199.0 | −5.043 |
Name | ΔGelec | ΔGvdW | ΔGnonp/sol | ΔGelec/sol | −TΔS | ΔGbind |
---|---|---|---|---|---|---|
Bz1 | −25.89 ± 0.09 | −13.88 ± 0.12 | −3.42 ± 0.01 | 24.14 ± 0.01 | 12.36 ± 0.28 | −6.69 ± 0.10 |
Bz2 | −25.11 ± 0.01 | −13.81 ± 0.12 | −3.45 ± 0.01 | 24.24 ± 0.03 | 12.61 ± 0.54 | −5.52 ± 0.14 |
Bz3 | −25.21 ± 0.11 | −14.33 ± 0.12 | −3.31 ± 0.01 | 23.23 ± 0.01 | 12.79 ± 0.31 | −6.83 ± 0.11 |
Bz4 | −26.21 ± 0.10 | −15.02 ± 0.13 | −3.28 ± 0.01 | 23.05 ± 0.04 | 12.38 ± 0.63 | −9.08 ± 0.18 |
Bz5 | −24.26 ± 0.11 | −13.52 ± 0.07 | −3.34 ± 0.01 | 23.51 ± 0.02 | 13.63 ± 0.55 | −4.68 ± 0.15 |
Bz6 | −26.03 ± 0.10 | −13.37 ± 0.16 | −3.18 ± 0.01 | 24.31 ± 0.02 | 14.25 ± 0.39 | −4.02 ± 0.14 |
Bz7 | −25.55 ± 0.08 | −13.78 ± 0.11 | −3.45 ± 0.01 | 24.61 ± 0.05 | 14.57 ± 0.71 | −3.60 ± 0.12 |
Bz8 | −25.16 ± 0.09 | −13.03 ± 0.13 | −3.04 ± 0.01 | 24.15 ± 0.03 | 13.69 ± 0.59 | −3.39 ± 0.17 |
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Kim, D.; Lee, D.-S. A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis. Int. J. Mol. Sci. 2010, 11, 3252-3265. https://doi.org/10.3390/ijms11093252
Kim D, Lee D-S. A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis. International Journal of Molecular Sciences. 2010; 11(9):3252-3265. https://doi.org/10.3390/ijms11093252
Chicago/Turabian StyleKim, Dooil, and Dae-Sil Lee. 2010. "A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis" International Journal of Molecular Sciences 11, no. 9: 3252-3265. https://doi.org/10.3390/ijms11093252