Theoretical Drug Design And Selectivity Mechanism Study Of Nek2 Inhibitors

Nek2(NIMA,Never-in-mitosis A-related kinase 2)is a serine/threonine protein kinase,which plays a key role in cell cycle regulation.Overexpression of Nek2 has been observed in several types of carcinoma revealed by a variety of studies,and overexpression of Nek2 can result in chromosomal instability(CIN),abnormal cell proliferation and several cell mitosis errors.In the meanwhile,Nek2 is also involved in drug resistance and poor prognosis of cancer patients.All of these evidence suggest that it is a potential target for cancer therapy.Therefore,it is of great significance to design and develop highly active and selective Nek2 inhibitors.Currently,the development of inhibitors for Nek2 is still in the initial stage,and the reported inhibitors have problems such as weak activity,low selectivity and poor pharmacokinetic properties.Therefore,in this study,multiple molecular simulation methods were employed to reveal the interactions between inhibitors and Nek2 and characterize the selective mechanism of Nek2 inhibitors,which may provide valuable information to design potent and selective Nek2 inhibitors.In the first part,we attempted to gain more insight into the binding mechanisms of a series of aminopyrazine inhibitors of Nek2 through molecular docking,molecular dynamic(MD)simulations and free energy calculations.The simulation results showed that the induced fit docking and ensemble docking based on multiple receptor conformations yield better predictions than conventional rigid receptor docking,highlighting the importance of incorporating receptor flexibility into the accurate predictions of the binding poses and binding affinities of Nek2 inhibitors.Additionally,we observed that the Molecular Mechanics/Generalized Born Surface Area(MM/GBSA)calculations did not show better performance than the docking scoring to rank the binding affinities of the studied inhibitors,suggesting that MM/GBSA is system-dependent and may not be the best choice for the Nek2 systems.Moreover,the detailed information on protein-ligand binding was characterized by the MM/GBSA free energy decomposition,and a number of derivatives with improved docking scores were designed.It is expected that our study can provide valuable information for the future rational design of novel and potent inhibitors of Nek2.In the second part,MD simulations,MM/GBSA free energy calculation and Umbrella Sampling(US)were employed to reveal the binding preference of three inhibitors towards Nek2,Plkl and CDK2,and to obtain the key information that may be helpful for the design of selective Nek2 inhibitors.The results showed that both of the binding free energies predicted by MM/GBSA and the PMF(Potential of the Mean Force)values calculated by US were consistent with the experimental data,indicating that these two calculation methods were suitable for our system.In addition,the pathway of each inhibitor dissociating from the active pocket was further revealed by the US results.The information obtained in this study may provide clues to design Nek2 inhibitors with improved selectivity.