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Title |
Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked to solanesol as an anti-cancer agent
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Authors |
Betty Daneial1, Jacob Paul Vazhappilly Joseph1, Guruprasad Ramakrishna2
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Affiliation |
1Botany Department, St. Joseph’s College, Bangalore 560027, Karnataka, India; 2Durga Femto Technologies and Research, Bangalore 560018, Karnataka, India;
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Article Type |
Hypothesis
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Date |
Received October 28, 2016; Accepted November 21, 2016; Published September 22, 2017
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Abstract |
Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding.
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Keywords: |
FAK; solanesol; angiogenesis; blind docking; contact scoring; GROMACS
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Citation |
Daneial et al. Bioinformation 13(9): 274-283 (2017)
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
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