In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules
Abstract
:1. Introduction
2. Results and Discussion
2.1. Molecular Dynamics Simulation
2.2. Pharmacophore Modelling
2.3. Virtual Screening
2.4. Molecular Docking, Rescoring and MD Simulation
3. Materials and Methods
3.1. Molecular Dynamics Simulation and Clustering
3.2. Pharmacophore Modelling and Virtual Screening
3.3. Docking and Rescoring
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Receptor | Native Ligand | Coordinates of Grid Center | Dimensions of the Outer Box (Å) | Dimensions of the Inner Box (Å) |
---|---|---|---|---|
FKBP12-FRB domain (PDB code 1FAP) | Rapamycin | X = −8.777 Y = 26.997 Z = 36.484 | X = 27.539 Y = 27.539 Z = 27.539 | X = 10 Y = 10 Z = 10 |
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Vittorio, S.; Gitto, R.; Adornato, I.; Russo, E.; De Luca, L. In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules. Molecules 2021, 26, 1103. https://doi.org/10.3390/molecules26041103
Vittorio S, Gitto R, Adornato I, Russo E, De Luca L. In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules. Molecules. 2021; 26(4):1103. https://doi.org/10.3390/molecules26041103
Chicago/Turabian StyleVittorio, Serena, Rosaria Gitto, Ilenia Adornato, Emilio Russo, and Laura De Luca. 2021. "In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules" Molecules 26, no. 4: 1103. https://doi.org/10.3390/molecules26041103