The mutant KRAS was considered as an “undruggable” target for decades, especially KRAS^G12D. It is a great challenge to develop the inhibitors for KRAS^G12D which lacks the thiol group for covalently binding ligands. The discovery of MRTX1133 solved the dilemma. Interestingly, MRTX1133 can bind to both the inactive and active states of KRAS^G12D. The binding mechanism of MRTX1133 with KRAS^G12D, especially how MRTX1133 could bind the active state KRAS^G12D without triggering the active function of KRAS^G12D_, has not been fully understood. Here, we used a combination of all-atom molecular dynamics simulations and Markov state model (MSM) to understand the inhibition mechanism of MRTX1133 and its analogs. The stationary probabilities derived from MSM show that MRTX1133 and its analogs can stabilize the inactive or active states of KRAS^G12D into different conformations. More remarkably, by scrutinizing the conformational differences, MRTX1133 and its analogs were hydrogen bonded to Gly60 to stabilize the switch II region and left switch I region in a dynamically inactive conformation, thus achieving an inhibitory effect. Our simulation and analysis provide detailed inhibition mechanism of KRAS^G12D induced by MRTX1133 and its analogs. This study will provide guidance for future design of novel small molecule inhibitors of KRAS^G12D.

几十年来，突变体 KRAS 一直被认为是“不可药性”的靶标，尤其是 KRAS ^G12D。开发缺乏用于共价结合配体的硫醇基团的 KRAS ^G12D抑制剂是一个巨大的挑战。MRTX1133的发现解决了这个困境。有趣的是，MRTX1133 可以结合 KRAS ^G12D的非活性和活性状态。^{MRTX1133与KRAS G12D}的结合机制，特别是MRTX1133如何在不触发KRAS ^G12D活性功能的情况下结合活性状态KRAS ^G12D _，还没有被完全理解。在这里，我们结合使用全原子分子动力学模拟和马尔可夫状态模型 (MSM) 来了解 MRTX1133 及其类似物的抑制机制。来自 MSM 的稳态概率表明 MRTX1133 及其类似物可以将 KRAS ^G12D的非活性或活性状态稳定为不同的构象。更值得注意的是，通过仔细检查构象差异，MRTX1133 及其类似物与 Gly60 形成氢键，以稳定开关 II 区域，并使开关 I 区域处于动态非活性构象中，从而实现抑制作用。^{我们的模拟和分析提供了 KRAS G12D}的详细抑制机制由 MRTX1133 及其类似物诱导。本研究将为未来设计新型KRAS ^G12D小分子抑制剂提供指导。