Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling

Anaplastic lymphoma kinase (ALK) has been regarded as a promising drug target in the treatment of tumors and the mutation L1196M induces different levels of drug resistance toward the existing inhibitors. Free energy perturbation (FEP) coupled with umbrella sampling simulation is used to investigate the conformational change of ALK induced by L1196M and drug-resistant mechanisms of L1196M on four inhibitors VGH, 3U9, 5P8 and IV7. Dynamics analysis shows that L119M produces significant influences on the flexibility of the loops L1 and L2 in ALK. FEP calculations suggest that the drug-resistant intensity of L1196M toward inhibitors decreases in the order 3U9 > VGH > 5P8 > IV7, in accordance with the experimentally determined results. Moreover, statistical analysis of hydrophobic contacts of inhibitors with separate residues in ALK further demonstrates that the decrease in the hydrophobic interactions of inhibitors with L1256 mostly drives drug resistance of L1196M toward inhibitors. The calculations of potential of mean force (PMF) based on umbrella sampling simulations indicate that the free energies of inhibitor-L1196M ALKs are lower than those of inhibitor-wild ALKs. This study is expected to provide significant theoretical support which would help in the design of potent inhibitors alleviating the drug resistance of L1196M in ALK.