Cheng Yuhui, Cheng Xiaolin, Radić Zoran, McCammon J Andrew
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0365, USA.
J Am Chem Soc. 2007 May 23;129(20):6562-70. doi: 10.1021/ja070601r. Epub 2007 Apr 27.
The reaction mechanisms of two inhibitors TFK+ and TFK0 binding to both the wild-type and H447I mutant mouse acetylcholinesterase (mAChE) have been investigated by using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach and classical molecular dynamics (MD) simulations. In the wild-type mAChE, the binding reactions of TFK+ and TFK0 are both spontaneous processes, which proceed through the nucleophilic addition of the Ser203-Ogamma to the carbonyl-C of TFK+ or TFK0, accompanied with a simultaneous proton transfer from Ser203 to His447. No barrier is found along the reaction paths, consistent with the experimental reaction rates approaching the diffusion-controlled limit. By contrast, TFK+ binding to the H447I mutant may proceed with a different reaction mechanism. A water molecule takes over the role of His447 and participates in the bond breaking and forming as a "charge relayer". Unlike in the wild-type mAChE case, Glu334, a conserved residue from the catalytic triad, acts as a catalytic base in the reaction. The calculated energy barrier for this reaction is about 8 kcal/mol. These predictions await experimental verification. In the case of the neutral ligand TFK0, however, multiple MD simulations on the TFK0/H447I complex reveal that none of the water molecules can be retained in the active site as a "catalytic" water. Furthermore, our alchemical free energy calculation also suggests that the binding of TFK0 to H447I is much weaker than that of TFK+. Taken together, our computational studies confirm that TFK0 is almost inactive in the H447I mutant and also provide detailed mechanistic insights into the experimental observations.
采用量子力学/分子力学（QM/MM）结合从头算方法和经典分子动力学（MD）模拟，研究了两种抑制剂TFK +和TFK0与野生型和H447I突变型小鼠乙酰胆碱酯酶（mAChE）的反应机制。在野生型mAChE中，TFK +和TFK0的结合反应均为自发过程，通过Ser203 - Oγ对TFK +或TFK0的羰基 - C进行亲核加成，同时伴随着质子从Ser203转移至His447。在反应路径上未发现能垒，这与实验反应速率接近扩散控制极限一致。相比之下，TFK +与H447I突变体的结合可能通过不同的反应机制进行。一个水分子取代了His447的作用，并作为“电荷中继体”参与键的断裂和形成。与野生型mAChE的情况不同，催化三联体中的保守残基Glu334在反应中充当催化碱。该反应的计算能垒约为8千卡/摩尔。这些预测有待实验验证。然而，对于中性配体TFK0，对TFK0/H447I复合物进行的多次MD模拟表明，没有水分子能够作为“催化”水保留在活性位点。此外，我们的炼金术自由能计算还表明，TFK0与H447I的结合比TFK +弱得多。综上所述，我们的计算研究证实TFK0在H447I突变体中几乎无活性，并为实验观察提供了详细的机制见解。
