Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease
Abstract
:1. Introduction
2. Results and Discussion
2.1. Homology Modeling and Molecular Dynamics Simulation
2.2. Modeling of Small Molecules Binding to the Human XPF Active Site
2.3. Virtual Screening
3. Materials and Methods
3.1. Homology Modeling of the Human XPF Nuclease Domain
3.2. Molecular Dynamics Simulation and Clustering of the Trajectory
3.3. Molecular Docking of Known Inhibitors and Pharmacophore Modeling
3.4. Virtual Screening of the ZINC15 Database
4. Conclusions
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Substitution Matrix | Top Templates | Others |
---|---|---|
BLOSUM50 | 2BGW, 2BHN | 1J22, 2ZIU, 4P0P |
BLOSUM62 | 2BGW, 2BHN, 1J22 | 2ZIU, 2ZIX, 4P0P |
Gonnet | 2BGW, 2BHN | 1J22 |
PAM250 | 2BGW, 2BHN | 1J22 |
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Gentile, F.; Barakat, K.H.; Tuszynski, J.A. Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease. Int. J. Mol. Sci. 2018, 19, 1328. https://doi.org/10.3390/ijms19051328
Gentile F, Barakat KH, Tuszynski JA. Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease. International Journal of Molecular Sciences. 2018; 19(5):1328. https://doi.org/10.3390/ijms19051328
Chicago/Turabian StyleGentile, Francesco, Khaled H. Barakat, and Jack A. Tuszynski. 2018. "Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease" International Journal of Molecular Sciences 19, no. 5: 1328. https://doi.org/10.3390/ijms19051328