Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077, Toulouse, France.
Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
Sci Rep. 2023 Oct 26;13(1):18399. doi: 10.1038/s41598-023-45272-3.
Inhibiting protein-protein interactions of the Myc family is a viable pharmacological strategy for modulation of the levels of Myc oncoproteins in cancer. Aurora A kinase (AurA) and N-Myc interaction is one of the most attractive targets of this strategy because formation of this complex blocks proteasomal degradation of N-Myc in neuroblastoma. Two crystallization studies have captured this complex (PDB IDs: 5g1x, 7ztl), partially resolving the AurA interaction region (AIR) of N-Myc. Prompted by the missing N-Myc fragment in these crystal structures, we modeled the complete structure between AurA and N-Myc, and comprehensively analyzed how the incomplete and complete N-Myc behave in complex by molecular dynamics simulations. Molecular dynamics simulations of the incomplete PDB complex (5g1x) repeatedly showed partial dissociation of the short N-Myc fragment (61-89) from the kinase. The missing N-Myc (19-60) fragment was modeled utilizing the N-terminal lobe of AurA as the protein-protein interaction surface, wherein TPX2, a well-known partner of AurA, also binds. Binding free energy calculations along with flexibility analysis confirmed that the complete AIR of N-Myc stabilizes the complex, accentuating the N-terminal lobe of AurA as a binding site for the missing N-Myc fragment (19-60). We further generated additional models consisting of only the missing N-Myc (19-60), and the fused form of TPX2 (7-43) and N-Myc (61-89). These partners also formed more stable interactions with the N-terminal lobe of AurA than did the incomplete N-Myc fragment (61-89) in the 5g1x complex. Altogether, this study provides structural insights into the involvement of the N-terminus of the AIR of N-Myc and the N-terminal lobe of AurA in formation of a stable complex, reflecting its potential for effective targeting of N-Myc.
抑制 Myc 家族的蛋白-蛋白相互作用是调节癌症中 Myc 癌蛋白水平的可行的药理学策略。Aurora A 激酶 (AurA) 和 N-Myc 相互作用是该策略最有吸引力的靶标之一，因为形成这种复合物会阻止神经母细胞瘤中 N-Myc 的蛋白酶体降解。两项晶体学研究捕获了这个复合物（PDB ID：5g1x、7ztl），部分解析了 N-Myc 的 AurA 相互作用区域 (AIR)。受这些晶体结构中缺失的 N-Myc 片段的启发，我们对 AurA 和 N-Myc 之间的完整结构进行了建模，并通过分子动力学模拟全面分析了不完整和完整的 N-Myc 在复合物中的行为。对不完整的 PDB 复合物（5g1x）的分子动力学模拟反复显示短 N-Myc 片段（61-89）从激酶中部分解离。缺失的 N-Myc（19-60）片段利用 AurA 的 N 端结构域作为蛋白-蛋白相互作用表面进行建模，其中 AurA 的一个众所周知的伴侣 TPX2 也结合在该表面。结合自由能计算和灵活性分析证实，完整的 N-Myc AIR 稳定了复合物，突出了 AurA 的 N 端结构域作为缺失的 N-Myc 片段（19-60）的结合位点。我们进一步生成了仅由缺失的 N-Myc（19-60）组成的额外模型，以及 TPX2（7-43）和 N-Myc（61-89）融合形式的模型。与 5g1x 复合物中不完整的 N-Myc 片段（61-89）相比，这些配体与 AurA 的 N 端结构域形成了更稳定的相互作用。总的来说，这项研究提供了结构上的见解，即 N-Myc 的 AIR 的 N 端和 AurA 的 N 端结构域参与形成稳定的复合物，反映了其有效靶向 N-Myc 的潜力。
