Abstract
Neuroblastoma is the most common and deadliest tumor in infancy. WDR5 (WD Repeat Domain 5), a critical factor supporting an N-myc transcriptional complex via its WBM site and interacting with chromosome via its WIN site, promotes the progression of neuroblastoma, thus making it a potential anti-neuroblastoma drug target. So far, a few WIN site inhibitors have been reported, and the WBM site disruptors are rare to see. In this study we conducted virtual screening to identify candidate hit compounds targeting the WBM site of WDR5. As a result, 60 compounds were selected as candidate WBM site inhibitors. Cell proliferation assay demonstrated 6 structurally distinct WBM site inhibitors, numbering as compounds 4, 7, 11, 13, 19 and 22, which potently suppressed 3 neuroblastoma cell lines (MYCN-amplified IMR32 and LAN5 cell lines, and MYCN-unamplified SK-N-AS cell line). Among them, compound 19 suppressed the proliferation of IMR32 and LAN5 cells with EC50 values of 12.34 and 14.89 μM, respectively, and exerted a moderate inhibition on SK-N-AS cells, without affecting HEK293T cells at 20 μM. Analysis of high-resolution crystal complex structure of compound 19 against WDR5 revealed that it competitively occupied the hydrophobic pocket where V264 was located, which might disrupt the interaction of MYC with WDR5 and further MYC-medicated gene transcription. By performing RNA-seq analysis we demonstrated the differences in molecular action mechanisms of the compound 19 and a WIN site inhibitor OICR-9429. Most interestingly, we established the particularly high synergy rate by combining WBM site inhibitor 19 and the WIN site inhibitor OICR-9429, providing a novel therapeutic avenue for neuroblastoma.
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Acknowledgements
This study was sponsored by Shanghai Municipal Science and Technology Commission (21Y11912200 to Kai Li), the Cyrus Tang Foundation, Clinical Research Plan of SHDC (SHDC2020CR2009A), Shanghai Municipal Key Clinical Specialty (shslczdzk05703), Hengjie Special Support Plan (2022 to Kai Li), Lingang Laboratory (LG202102-01-03), National Natural Science Foundation of China (82003654), Shanghai Science and Technology Development Funds (20QA1406400), and the Science and Technology Commission of Shanghai Municipality Grants (20431900100, 2043190012 and 20430780300); as well as the startup package from ShanghaiTech University. We also thank the HPC Platform of ShanghaiTech University and Shanghai Supercomputer Center for computing time.
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FB, KL, and LHM conceptualized and designed the study. PXR and LW performed virtual screening. QLH, XLZ, YC, and WHL performed molecular biology experiments and analyzed the data. QLH and XLZ drafted the manuscript, which was revised and embellished by FB. FB, and KL supervised the study. All authors read and approved the article.
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Han, Ql., Zhang, Xl., Ren, Px. et al. Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma. Acta Pharmacol Sin 44, 877–887 (2023). https://doi.org/10.1038/s41401-022-00999-z
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DOI: https://doi.org/10.1038/s41401-022-00999-z
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