Computational studies of potent covalent inhibitors on wild type or T790M/L858R mutant epidermal growth factor receptor

In this paper, we designed and synthesized two analog compounds M1 and T1 that have a Michael acceptor warhead. Although only slightly diversity existed in the structures of M1 and T1, their inhibitory activities against wild type epidermal growth factor receptor (EGFR(WT)) and (T790M/L858R) mutant epidermal growth factor receptor (EGFR(T790M/L858R)) were significant different. Thus, multiple computational approaches were applied to investigate the interactions between the compounds with EGFR(WT) and EGFRT(790M/L858R) in order to explore the effect of different compounds. The molecular docking and MD simulations were performed to study the intermolecular interactions between compounds and EGFR. The binding free energy revealed that M1-EGFR(WT) and M1-EGFRT(790M/L858R) complexes have stronger binding affinity compared with the corresponding T1-EGFR(WT) and T1-EGFR(T790M/L858R) complexes, respectively. And the binding free energy decompositions for each residue analysis indicated that the van der Waals interactions are the major contributor to enhance the compounds to bind with EGFR. In addition, covalent binding complexes of M1-EGFR(WT) and M1-EGFRT(790M/L858R) were constructed and studied. Moreover, quantum mechanics method was applied to investigate the reaction mechanism of covalent binding of the compound and EGFR. The results will provide the details of structural and energetic information to develop potent covalent EGFR inhibitors in the future.