3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors
Abstract
:1. Introduction
2 Results and Discussion
2.1. Pharmacophore Model Generation and Validation
2.2. CBP Pharmacophore Model-Based Virtual Screening
2.3. Molecular Docking
2.4. HipHop Pharmacophore Model-Based Virtual Screening
3. Materials and Methods
3.1. Data Collection and Preparation
3.2. Pharmacophore Model Generation
3.3. Pharmacophore-Based Virtual Screening
3.4. Molecular Docking
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sample Availability: Not available. |
Name | Structure | Binging Energy | LibDock Score | -CDOCKER Energy | Fit Value |
---|---|---|---|---|---|
Crystallographic ligand | −68.857 | 130.542 | 21.08 | 2.35 | |
L503-0533 | −130.39 | 151.48 | 31.75 | 2.75 | |
G622-0791 | −167.41 | 138.71 | 39.18 | 2.97 | |
G883-0326 | −125.71 | 141.43 | 21.93 | 2.56 | |
G883-0326 | −133.97 | 138.34 | 22.73 | 3.02 |
Structure | AlogP | Weight | Num-H Acceptors | Num-H Donors | Num-H Rotatable Bonds | Molecular Polar Surface Area | IC50 |
---|---|---|---|---|---|---|---|
3.429 | 444.54 | 7 | 2 | 6 | 104.32 | - | |
2.53 | 329.23 | 5 | 0 | 4 | 97.03 | 0.28 | |
2.216 | 372.82 | 6 | 0 | 5 | 102.95 | 0.01 | |
2.827 | 369.39 | 7 | 2 | 4 | 137.48 | 0.01 | |
1.883 | 328.77 | 5 | 1 | 3 | 93.72 | 0.01 | |
2.336 | 442.91 | 7 | 1 | 7 | 115.35 | 0.01 | |
1.965 | 458.91 | 8 | 1 | 6 | 124.57 | 0.04 | |
3.086 | 445.55 | 4 | 1 | 6 | 78.09 | - | |
3.371 | 417.43 | 4 | 1 | 6 | 71.53 | - | |
4.659 | 384.47 | 2 | 1 | 4 | 49.41 | - | |
3.629 | 391.85 | 3 | 1 | 4 | 62.3 | - |
Hypothesis | Features | Rank |
---|---|---|
HipHop-Hypo1 | RHAAAA | 81.854 |
HipHop-Hypo2 | RHAAAA | 81.854 |
HipHop-Hypo3 | RHAAAA | 81.788 |
HipHop-Hypo4 | RAAAA | 72.750 |
HipHop-Hypo5 | RAAAA | 72.347 |
HipHop-Hypo6 | RAAAA | 72.293 |
HipHop-Hypo7 | RAAAA | 72.234 |
HipHop-Hypo8 | RAAAA | 72.188 |
HipHop-Hypo9 | RAAAA | 72.188 |
HipHop-Hypo10 | RAAAA | 72.167 |
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Fu, Y.; Sun, Y.-N.; Yi, K.-H.; Li, M.-Q.; Cao, H.-F.; Li, J.-Z.; Ye, F. 3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors. Molecules 2017, 22, 959. https://doi.org/10.3390/molecules22060959
Fu Y, Sun Y-N, Yi K-H, Li M-Q, Cao H-F, Li J-Z, Ye F. 3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors. Molecules. 2017; 22(6):959. https://doi.org/10.3390/molecules22060959
Chicago/Turabian StyleFu, Ying, Yi-Na Sun, Ke-Han Yi, Ming-Qiang Li, Hai-Feng Cao, Jia-Zhong Li, and Fei Ye. 2017. "3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors" Molecules 22, no. 6: 959. https://doi.org/10.3390/molecules22060959