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<p>The upregulation of interleukin-1 receptor-associated kinase 4 (<i>IRAK4</i>) drives pro-tumorigenic signaling across various malignancies. Currently available <i>IRAK4</i> inhibitors are all limited by suboptimal selectivity and off-target toxicity. To develop non-toxic and mechanistically focused <i>IRAK4</i> inhibitors, an in silico machine learning (ML) pipeline combined with structure-driven drug repositioning was employed. An <i>IRAK4</i>-targeting dataset of bioactive compounds was systematically filtered and curated to train a random forest (RF) regression model. Comparative cross-validation against 41 independent ML frameworks demonstrated reasonable predictive accuracy, and the optimized model was deployed to screen a library of 1040 FDA-approved therapeutics. Orthogonal molecular docking supported the binding efficacy of RF-identified lead compounds, including udenafil, linagliptin, benflumetol, and nimodipine. Thermodynamic and conformational stability were validated using molecular dynamics (MD) simulations, yielding stable root mean square deviation (RMSD), radius of gyration (<i>R</i><sub>g</sub>), root mean square fluctuation (RMSF), principal component analysis (PCA), hydrogen bonding, and MMGBSA/MM-PBSA profiles. The efficacy of these candidates was further supported by their low toxicity profiles, via graph neural network (GNN)-based toxicity analysis. These findings establish a scalable computational strategy for identifying repurposable oncology therapeutics and propose udenafil, linagliptin, benflumetol, and nimodipine as mechanistically credible candidates for experimental validation.</p>

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An integrative machine learning and structure-driven drug repositioning strategy for human IRAK4-targeted cancer therapy

  • 期刊论文

  • 发表日期：

    2026年4月30日

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  • Muhammad Waleed Iqbal,
  • Muhammad Ali Raza,
  • Muneer Ahmad,
  • Xinxiao Sun,
  • Jianlong Lv,
  • Xiaolin Shen

摘要

The upregulation of interleukin-1 receptor-associated kinase 4 (IRAK4) drives pro-tumorigenic signaling across various malignancies. Currently available IRAK4 inhibitors are all limited by suboptimal selectivity and off-target toxicity. To develop non-toxic and mechanistically focused IRAK4 inhibitors, an in silico machine learning (ML) pipeline combined with structure-driven drug repositioning was employed. An IRAK4-targeting dataset of bioactive compounds was systematically filtered and curated to train a random forest (RF) regression model. Comparative cross-validation against 41 independent ML frameworks demonstrated reasonable predictive accuracy, and the optimized model was deployed to screen a library of 1040 FDA-approved therapeutics. Orthogonal molecular docking supported the binding efficacy of RF-identified lead compounds, including udenafil, linagliptin, benflumetol, and nimodipine. Thermodynamic and conformational stability were validated using molecular dynamics (MD) simulations, yielding stable root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF), principal component analysis (PCA), hydrogen bonding, and MMGBSA/MM-PBSA profiles. The efficacy of these candidates was further supported by their low toxicity profiles, via graph neural network (GNN)-based toxicity analysis. These findings establish a scalable computational strategy for identifying repurposable oncology therapeutics and propose udenafil, linagliptin, benflumetol, and nimodipine as mechanistically credible candidates for experimental validation.