Complex Crystal Structure Determination and in vitro Anti–non–small Cell Lung Cancer Activity of Hsp90N Inhibitor SNX-2112

Abstract

SNX-2112, as a promising anticancer lead compound targeting heat shock protein 90 (Hsp90), absence of complex crystal structure of Hsp90N-SNX-2112 hindered further structural optimization and understanding on molecular interaction mechanism. Herein, a high-resolution complex crystal structure of Hsp90N-SNX-2112 was successfully determined by X-ray diffraction, resolution limit, 2.14 Å, PDB ID 6LTK, and their molecular interaction was analyzed in detail, which suggested that SNX-2112 was well accommodated in the ATP-binding pocket to disable molecular chaperone activity of Hsp90, therefore exhibiting favorable inhibiting activity on three non–small cell lung cancer (NSCLC) cell lines (IC50, 0.50 ± 0.01 μM for A549, 1.14 ± 1.11 μM for H1299, 2.36 ± 0.82 μM for H1975) by inhibited proliferation, induced cell cycle arrest, and aggravated cell apoptosis. SNX-2112 exhibited high affinity and beneficial thermodynamic changes during the binding process with its target Hsp90N confirmed by thermal shift assay (TSA, ΔTm, and −9.51 ± 1.00°C) and isothermal titration calorimetry (Kd, 14.10 ± 1.60 nM). Based on the complex crystal structure and molecular interaction analysis, 32 novel SNX-2112 derivatives were designed, and 25 new ones displayed increased binding force with the target Hsp90N verified by molecular docking evaluation. The results would provide new references and guides for anti-NSCLC new drug development based on the lead compound SNX-2112.

Novel matrinic acid derivatives bearing 2‐anilinothiazole structure for non‐small cell lung cancer treatment with improved Hsp90 targeting effect

“…As illustrated in Figure 4, Hsp90 showed a melting point of 47.68 ± 0.46°C, while the complex of C4 and hsp90 was 28.47 ± 0.48°C. The marked changes of Δ T m (−18.85 ± 0.56°C) demonstrated that C4 exhibited high affinity with Hsp90, even better than SNX‐2112 (−9.51 ± 1.00°C) (D. Zhao et al, 2021), 22g (10.92 ± 0.60°C) (Xu et al, 2020) and comparable with radicicol (21.32 ± 0.29°C). However, the Δ T m caused by matrine was only 0.04 ± 0.39°C.…”

Comparative Study of the Crystal Structure and Simulated 3D Structure of the Hsp90N‐Inhibitor Complex

“…In the early stage, our group successfully determined the complex crystal structures of the target Hsp90 N and its four small molecule inhibitors. [3,4,16,17] In this study, computer-aided molecular docking technology was applied to predict the complex 3D structures of the target Hsp90 N and its four inhibitors. Moreover, the comparison between the simulated 3D structures and crystal structures was thoroughly analyzed.…”

“…[11] The discovery of Hsp90 inhibitors has been an important strategy for new anticancer drug development. [12][13][14][15] Previously, the crystal structures of four small molecule inhibitors (Debio0932, SNX-2112, KW-2478, and NVP-AUY922) and Hsp90 N have been successfully determined by our group, [3,4,16,17] which would promote structural optimization of inhibitors and deepen the understanding of molecular mechanisms behind Hsp90. Herein, Sybyl software was applied to build the simulated 3D structure of the four abovementioned inhibitors and Hsp90 N by molecular docking.…”