Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China.
Acta Crystallogr D Struct Biol. 2021 Jan 1;77(Pt 1):86-97. doi: 10.1107/S2059798320014990.
Debio0932 is a promising lead compound in phase I clinical trials targeting the N-terminal ATP-binding pocket of the molecular chaperone heat-shock protein 90 (Hsp90). The absence of a crystal structure of the Hsp90-Debio0932 complex, however, has impeded further structural optimization of Debio0932 and understanding of the molecular-interaction mechanism. Here, a high-resolution crystal structure of the Hsp90-Debio0932 complex was successfully determined (resolution limit 2.20 Å; PDB entry 6lr9) by X-ray diffraction and the molecular-interaction mechanism was analysed in detail, which suggested that Debio0932 suppresses cancer cells by accommodating itself in the ATP-binding pocket of Hsp90, disabling its molecular-chaperone capability. The results of a thermal shift assay (ΔT = 8.83 ± 0.90°C) and isothermal titration calorimetry (K = 15.50 ± 1.30 nM) indicated strong binding and favourable thermodynamic changes in the binding of Hsp90 and Debio0932. Based on the crystal structure of the complex and on molecular-interaction analysis, 30 new Debio0932 derivatives were designed and nine new derivatives exhibited increased binding to Hsp90, as determined by molecular-docking evaluation. Additionally, Debio0932 suppressed cell proliferation (IC values of 3.26 ± 2.82 µM for A549, 20.33 ± 5.39 µM for H1299 and 3.16 ± 1.04 µM for H1975), induced cell-cycle arrest and promoted apoptosis in three non-small-cell lung cancer (NSCLC) cell lines. These results provide novel perspectives and guidance for the development of new anti-NSCLC drugs based on the lead compound Debio0932.
Debio0932 是一种在针对分子伴侣热休克蛋白 90（Hsp90）N 端 ATP 结合口袋的 I 期临床试验中很有前途的先导化合物。然而，由于缺乏 Hsp90-Debio0932 复合物的晶体结构，进一步对 Debio0932 进行结构优化和理解分子相互作用机制受到了阻碍。在这里，通过 X 射线衍射成功地确定了 Hsp90-Debio0932 复合物的高分辨率晶体结构（分辨率限制为 2.20Å；PDB 条目 6lr9），并详细分析了分子相互作用机制，该机制表明 Debio0932 通过适应 Hsp90 的 ATP 结合口袋，使其无法发挥分子伴侣的能力，从而抑制癌细胞。热转移测定（ΔT = 8.83 ± 0.90°C）和等温滴定量热法（K = 15.50 ± 1.30 nM）的结果表明，Hsp90 和 Debio0932 之间的结合具有很强的结合力和有利的热力学变化。基于复合物的晶体结构和分子相互作用分析，设计了 30 种新的 Debio0932 衍生物，其中 9 种新衍生物在分子对接评价中表现出与 Hsp90 的结合增加。此外，Debio0932 抑制了三种非小细胞肺癌（NSCLC）细胞系的细胞增殖（A549 的 IC 值为 3.26 ± 2.82µM，H1299 为 20.33 ± 5.39µM，H1975 为 3.16 ± 1.04µM），诱导细胞周期停滞并促进凋亡。这些结果为基于先导化合物 Debio0932 开发新型抗 NSCLC 药物提供了新的视角和指导。
