Ramos-Guzmán Carlos A, Ruiz-Pernía J Javier, Tuñón Iñaki
Departamento de Química Física, Universidad de Valencia, Burjassot 46100, Spain.
ACS Catal. 2021 Apr 2;11(7):4157-4168. doi: 10.1021/acscatal.0c05522. Epub 2021 Mar 25.
We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those containing an aldehyde group as a warhead. These compounds are covalent inhibitors that inactivate the protease, forming a stable hemithioacetal complex. Inhibitor is a potent inhibitor that has been already tested in vitro and in animals. Using a combination of classical and QM/MM simulations, we determined the binding mode of the inhibitor into the active site and the preferred rotameric state of the catalytic histidine. In the noncovalent complex, the aldehyde group is accommodated into the oxyanion hole formed by the NH main-chain groups of residues 143 to 145. In this pose, P1-P3 groups of the inhibitor mimic the interactions established by the natural peptide substrate. The reaction is initiated with the formation of the catalytic dyad ion pair after a proton transfer from Cys145 to His41. From this activated state, covalent inhibition proceeds with the nucleophilic attack of the deprotonated Sγ atom of Cys145 to the aldehyde carbon atom and a water-mediated proton transfer from the Nε atom of His41 to the aldehyde oxygen atom. Our proposed reaction transition-state structure is validated by comparison with X-ray data of recently reported inhibitors, while the activation free energy obtained from our simulations agrees with the experimentally derived value, supporting the validity of our findings. Our study stresses the interplay between the conformational dynamics of the inhibitor and the protein with the inhibition mechanism and the importance of including conformational diversity for accurate predictions about the inhibition of the main protease of SARS-CoV-2. The conclusions derived from our work can also be used to rationalize the behavior of other recently proposed inhibitor compounds, including aldehydes and ketones with high inhibitory potency.
我们在此研究最具潜力的抑制剂家族之一（即含有醛基作为弹头的抑制剂）对新型冠状病毒 3CL 蛋白酶的抑制机制。这些化合物是共价抑制剂，可使蛋白酶失活，形成稳定的半硫代缩醛复合物。抑制剂 是一种强效抑制剂，已在体外和动物体内进行过测试。通过结合经典模拟和量子力学/分子力学（QM/MM）模拟，我们确定了抑制剂在活性位点的结合模式以及催化组氨酸的优选旋转异构体状态。在非共价复合物中，醛基容纳在由残基 143 至 145 的 NH 主链基团形成的氧阴离子孔中。在此构象下，抑制剂的 P1 - P3 基团模拟天然肽底物建立的相互作用。反应始于质子从 Cys145 转移至 His41 后催化二元离子对的形成。从这种活化状态开始，共价抑制通过 Cys145 的去质子化 Sγ 原子对醛碳原子的亲核攻击以及水介导的质子从 His41 的 Nε 原子转移至醛氧原子而进行。我们提出的反应过渡态结构通过与最近报道的抑制剂的 X 射线数据进行比较得到验证，而从我们的模拟中获得的活化自由能与实验得出的值一致，支持了我们研究结果的有效性。我们的研究强调了抑制剂和蛋白质的构象动力学与抑制机制之间的相互作用，以及纳入构象多样性对于准确预测新型冠状病毒主要蛋白酶抑制作用的重要性。我们工作得出的结论还可用于解释其他最近提出的抑制剂化合物的行为，包括具有高抑制效力的醛和酮。
