A Combination of Molecular Docking, and Molecular Dynamics Simulation Studies of S-Trityl-L-Cysteine Analogues as Kinesin Eg5 Inhibitors

kinesin Eg5, a member of the kinesin-5 superfamily, is responsible for the formation and maintenance of bipolar spindle in the early stage of mitosis. Since Eg5 plays a crucial role in cell division, inhibition of this protein causes mitotic arrest, which can lead to cell death. Therefore it is an interesting drug target for the design of potent inhibitors. In the past few years, a large number of chemicals were synthesized and evaluated as Eg5 inhibitors[1, 2]. In the recent years, Kosielski and coworkers introduced S-trityl-L-cysteine (STLC) as a potent Eg5 inhibitor [3]. Due to its high efficiency, new analogues of STLC with improved activity against Eg5 were synthesized by Wang and coworkers [4]. In order to know the interaction between these new STLC analogues as inhibitors and Eg5 an investigation of molecular docking and MD simulation were carried out in this work, in which two inhibitors (Mol 1, and Mol 2) were selected .Molecular docking was carried out by using the AutoDock 4.2 program. Preparation of protein (PDB ID code: 2WOG) and ligand was done using the AutoDock Tools. we performed MD simulations on Eg5 and optimal docked structures of Eg5 with 2-(((3-ethylphenyl) diphenylmethyl)thio)ethan-1-amine (Mol 2) as the most potent inhibitor. MD simulations were performed with the NAMD 2.9 program using the CHARMM 22 force field. The results obtained from docking show the binding pocket of Eg5 is mainly contributed by residues Thr112, Ile136, Pro137, Leu132, Ala133, Asp130, Gly117, Arg221, Arg119, Leu214, Glu116, Ala218, Trp127, Glu118 and Tyr211, which are similar to residue in the active site of 2WOG. Obviously, it is observed that the hydrophobic interaction plays significant role in the binding of inhibitors to Eg5 because of the presence of phenyl groups. In addition, docking result showed the presence of strong hydrogen bond between inhibitors and protein residues. Besides, in order to further investigate the binding mode and the conformation change of Eg5-inhibitor complexes in the presence of solvent MD simulation of Eg5 and Eg5-Mol 2 complex with lowest docked energy were successfully run for 10 ns scale. The RMSD value of protein backbone with simulation time was assessed in order to explore the dynamic stability of the complex. According to Fig. 1 the RMSD of Eg5 and Eg5-Mol 2 complex reach equilibration and oscillates around in average value after 2 ns simulation time. This indicates that the trajectory of the MD simulation is stable after 2 ns, so, it is reasonable to investigate binding pocket based on the snapshot extracted from 2 to 10 ns