Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy.
J Chem Inf Model. 2015 Mar 23;55(3):589-99. doi: 10.1021/ci500720e. Epub 2015 Feb 17.
Irreversible epidermal growth factor receptor (EGFR) inhibitors can circumvent resistance to first-generation ATP-competitive inhibitors in the treatment of nonsmall-cell lung cancer. They covalently bind a noncatalytic cysteine (Cys797) at the surface of EGFR active site by an acrylamide warhead. Herein, we used a hybrid quantum mechanics/molecular mechanics (QM/MM) potential in combination with umbrella sampling in the path-collective variable space to investigate the mechanism of alkylation of Cys797 by the prototypical covalent inhibitor N-(4-anilinoquinazolin-6-yl) acrylamide. Calculations show that Cys797 reacts with the acrylamide group of the inhibitor through a direct addition mechanism, with Asp800 acting as a general base/general acid in distinct steps of the reaction. The obtained reaction free energy is negative (ΔA = -12 kcal/mol) consistent with the spontaneous and irreversible alkylation of Cys797 by N-(4-anilinoquinazolin-6-yl) acrylamide. Our calculations identify desolvation of Cys797 thiolate anion as a key step of the alkylation process, indicating that changes in the intrinsic reactivity of the acrylamide would have only a minor impact on the inhibitor potency.
不可逆表皮生长因子受体 (EGFR) 抑制剂可避免第一代 ATP 竞争性抑制剂在治疗非小细胞肺癌中的耐药性。它们通过丙烯酰胺弹头共价结合 EGFR 活性位点表面的非催化半胱氨酸 (Cys797)。在此，我们使用混合量子力学/分子力学 (QM/MM) 势能与路径集合变量空间中的伞状采样相结合，研究了原型共价抑制剂 N-(4-苯胺基喹唑啉-6-基)丙烯酰胺对 Cys797 的烷化机制。计算表明，Cys797 通过直接加成机制与抑制剂的丙烯酰胺基团反应，Asp800 在反应的不同步骤中充当通用碱/酸碱。获得的反应自由能为负（ΔA = -12 kcal/mol），与 N-(4-苯胺基喹唑啉-6-基)丙烯酰胺对 Cys797 的自发和不可逆烷化一致。我们的计算确定 Cys797 巯基阴离子的去溶剂化是烷化过程的关键步骤，表明丙烯酰胺的内在反应性变化对抑制剂效力的影响很小。
