Anaplastic lymphoma kinase (ALK) has been thought to be a prospective target of anti-drug resistance design in treatment of tumors and specific neuron diseases. It is highly useful for the seeking of possible strategy alleviating drug resistance to probe the mutation-mediated effect on binding of inhibitors to ALK. In the current work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations, molecular mechanics generalized Born surface area (MM-GBSA) and free energy landscapes were coupled to explore influences of mutations L1198F, L1198F/C1156Y, and C1156Y on the binding of the first ALK inhibitor crizotinib to ALK. The results suggest that three mutations obviously affect structural flexibility, motion modes and conformational changes of ALKs. L1198F and L1198F/C1156Y strengthen the binding of crizotinib to the mutated ALKs but C1156Y induces evident drug resistance toward crizotinib. Analyses of free energy landscapes show that stability in the orientation and positions of crizotinib relative to ALK plays a vital role in alleviating drug resistance of mutations toward crizotinib. Residue-based free energy decomposition method was utilized to evaluate the contributions of separate residues to the binding of crizotinib. The results not only indicate that the tuning of point mutation L1198F on interaction networks of crizotinib with ALK can be regarded as a possible strategy to relieve drug resistance of the mutated ALK but also further verify that residues L1122, V1130, L1196, L1198, M1199, and L1256 can be used as efficient targets of anti-drug resistance design induced by mutations.

间变性淋巴瘤激酶 (ALK) 被认为是治疗肿瘤和特定神经元疾病的抗药性设计的前瞻性目标。探索突变介导的抑制剂与 ALK 结合的影响对于寻找减轻耐药性的可能策略非常有用。在目前的工作中，多副本高斯加速分子动力学 (MR-GaMD) 模拟、分子力学广义玻恩表面积 (MM-GBSA) 和自由能景观相结合，探索突变 L1198F、L1198F/C1156Y 和 C1156Y 对第一种 ALK 抑制剂克唑替尼与 ALK 的结合。结果表明，三个突变明显影响ALKs的结构灵活性、运动模式和构象变化。L1198F ​​和 L1198F/C1156Y 加强了克唑替尼与突变 ALK 的结合，但 C1156Y 诱导了对克唑替尼的明显耐药性。对自由能景观的分析表明，克唑替尼相对于 ALK 的方向和位置的稳定性在减轻对克唑替尼的突变的耐药性方面起着至关重要的作用。利用基于残基的自由能分解方法来评估不同残基对克唑替尼结合的贡献。结果不仅表明点突变 L1198F ​​对克唑替尼与 ALK 相互作用网络的调节可作为缓解突变 ALK 耐药性的可能策略，而且进一步验证了残基 L1122、V1130、L1196、L1198、M1199、 L1256可作为突变诱导抗药性设计的有效靶点。