Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China;
Proc Natl Acad Sci U S A. 2021 Mar 16;118(11). doi: 10.1073/pnas.2024725118.
The prevalent view on whether Ras is druggable has gradually changed in the recent decade with the discovery of effective inhibitors binding to cryptic sites unseen in the native structures. Despite the promising advances, therapeutics development toward higher potency and specificity is challenged by the elusive nature of these binding pockets. Here we derive a conformational ensemble of guanosine diphosphate (GDP)-bound inactive Ras by integrating spin relaxation-validated atomistic simulation with NMR chemical shifts and residual dipolar couplings, which provides a quantitative delineation of the intrinsic dynamics up to the microsecond timescale. The experimentally informed ensemble unequivocally demonstrates the preformation of both surface-exposed and buried cryptic sites in Ras•GDP, advocating design of inhibition by targeting the transient druggable conformers that are invisible to conventional experimental methods. The viability of the ensemble-based rational design has been established by retrospective testing of the ability of the Ras•GDP ensemble to identify known ligands from decoys in virtual screening.
在最近十年中，随着发现能够结合到天然结构中未观察到的隐蔽结合位点的有效抑制剂，人们对 Ras 是否可成药的主流观点逐渐发生了变化。尽管取得了有希望的进展，但由于这些结合口袋的难以捉摸的性质，针对更高效力和特异性的治疗药物开发仍面临挑战。在这里，我们通过将经过自旋弛豫验证的原子模拟与 NMR 化学位移和残余偶极耦合相结合，推导出 GDP 结合的非活性 Ras 的构象集合，从而在微秒时间尺度上对固有动力学进行了定量描述。经过实验验证的集合明确证明了 Ras•GDP 中表面暴露和埋藏的隐蔽结合位点的预先形成，这为通过靶向传统实验方法无法检测到的瞬时成药构象来设计抑制剂提供了依据。通过对 Ras•GDP 集合识别虚拟筛选中诱饵中已知配体的能力进行回溯性测试，已经证明了基于集合的合理设计的可行性。
