Establishing wonder oil, Solanesol, as a novel inhibitor for Focal Adhesive Kinase by in silico strategies

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been implicated in a series of cellular processes, including cell migration and survival. Inhibiting the activity of FAK for cancer therapy is currently under investigation. Hence, FAK and its inhibitors has been the subject of intensive research. To understand the structural factors affecting inhibitory potency, kinetic analysis, molecular docking and molecular dynamics simulation were studied in this project. Though, Solanesol was found have inhibitory activities towards FAK, no in silico tests were ever done on the same.\n\nDue to high flexibility of Solanesol (Rotatable bonds = 25), it is difficult to analyze using normal docking protocols. This paper introduces a novel method to dock and analyze molecules with high flexibility based on weighed contact based scoring method. This method uses blind docking technique, which was developed for protein peptide docking method, to generate conformations which were used to calculate contact based weights of residues. This method reveals the possible binding site for the small molecule. An exhaustive docking search on the acquired area reveals the docked confirmation of the compound. The final docked conformation was subjected to molecular dynamics to understand of binding stability. This study is in a good agreement with experimental results which shows Solanesol binds at ATP binding site and inhibit the phosphorylation of Focal Adhesion Kinase.