Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling.
Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling.
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DOI：
10.1021/acs.biochem.3c00378
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发表时间：
2023-11
期刊：
影响因子：
2.9
通讯作者：
Robert J Brenner;Alexander D Landgraf;K. Bum-Erdene;Giovanni Gonzalez-Gutierrez;S. Meroueh
中科院分区：
文献类型：
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作者：
Robert J Brenner;Alexander D Landgraf;K. Bum-Erdene;Giovanni Gonzalez-Gutierrez;S. Meroueh
KRAS GTP酶在超过25%的人类肿瘤中具有致癌突变。由于缺乏合适的小分子结合位点，KRAS被认为在很大程度上是不可用药的。在这里，我们报告了一个独特的晶体结构的组氨酸标记的KRASG 12 D，揭示了显着的构象变化。一个His-KRASG 12 D结构的开关I环延伸到相邻单位细胞中另一个His-KRASG 12 D的开关I/II口袋中，以创建一个复杂的界面，让人联想到高亲和力蛋白质-蛋白质复合物。我们使用丙氨酸扫描研究和基于显式溶剂分子动力学模拟的炼金术自由能微扰计算来探索氨基酸在该界面上的贡献。发现几种界面氨基酸是热点，因为它们对蛋白质-蛋白质相互作用的贡献超过1.5 kcal/mol。对复合物的计算分析揭示了两个大的结合口袋的存在，所述结合口袋具有通常在被认为可药用的口袋中发现的物理化学特征。如果KRAS存在于细胞中，则与这些口袋结合的小分子可以稳定KRAS的这种自抑制结构，从而提供抑制RAS信号传导的新策略。
KRAS GTPases harbor oncogenic mutations in more than 25% of human tumors. KRAS is considered to be largely undruggable due to the lack of a suitable small-molecule binding site. Here, we report a unique crystal structure of His-tagged KRASG12D that reveals a remarkable conformational change. The Switch I loop of one His-KRASG12D structure extends into the Switch I/II pocket of another His-KRASG12D in an adjacent unit cell to create an elaborate interface that is reminiscent of high-affinity protein-protein complexes. We explore the contributions of amino acids at this interface using alanine-scanning studies with alchemical free energy perturbation calculations based on explicit-solvent molecular dynamics simulations. Several interface amino acids were found to be hot spots as they contributed more than 1.5 kcal/mol to the protein-protein interaction. Computational analysis of the complex revealed the presence of two large binding pockets that possess physicochemical features typically found in pockets considered druggable. Small-molecule binding to these pockets may stabilize this autoinhibited structure of KRAS if it exists in cells to provide a new strategy to inhibit RAS signaling.