Cirino Thalita, Pinto Luis, Iwan Mateusz, Dougha Alexis, Lučić Bono, Kraljević Antonija, Navoyan Zaven, Tevosyan Ani, Yeghiazaryan Hrach, Khondkaryan Lusine, Abelyan Narek, Atoyan Vahe, Babayan Nelly, Iwashita Yuma, Kimura Kyosuke, Komasaka Tomoya, Shishido Koki, Nakamura Taichi, Asada Mizuho, Jain Sankalp, Zakharov Alexey V, Wang Haobo, Liu Wenjia, Chupakhin Vladimir, Uesawa Yoshihiro
Molecular Biotechnology and Health Sciences Department, University of Turin, Turin 10126, Italy.
Independent Researcher, Montreal H2Y 3Z2, Canada.
Chem Res Toxicol. 2025 May 15. doi: 10.1021/acs.chemrestox.5c00018.
Transthyretin (TTR) is a key transporter of the thyroid hormone thyroxine, and chemicals that bind to TTR, displacing the hormone, can disrupt the endocrine system, even at low concentrations. This study evaluates computational modeling strategies developed during the Tox24 Challenge, using a data set of 1512 compounds tested for TTR binding affinity. Individual models from nine top-performing teams were analyzed for performance and uncertainty using regression metrics and applicability domains (AD). Consensus models were developed by averaging predictions across these models, with and without consideration of their ADs. While applying AD constraints in individual models generally improved external prediction accuracy (at the expense of reduced chemical space coverage), it had limited additional benefit for consensus models. Results showed that consensus models outperformed individual models, achieving a root-mean-square error (RMSE) of 19.8% on the test set, compared to an average RMSE of 20.9% for the nine individual models. Outliers consistently identified in several of these models indicate potential experimental artifacts and/or activity cliffs, requiring further investigation. Substructure importance analysis revealed that models prioritized different chemical features, and consensus averaging harmonized these divergent perspectives. These findings highlight the value of consensus modeling in improving predictive performance and addressing model limitations. Future work should focus on expanding chemical space coverage and refining experimental data sets to support public health protection.
转甲状腺素蛋白(TTR)是甲状腺激素甲状腺素的关键转运蛋白,与TTR结合并取代该激素的化学物质,即使在低浓度下也能扰乱内分泌系统。本研究使用1512种化合物的数据集评估了在Tox24挑战赛期间开发的计算建模策略,这些化合物针对TTR结合亲和力进行了测试。使用回归指标和适用域(AD)分析了九个表现最佳团队的单个模型的性能和不确定性。通过对这些模型的预测进行平均来开发共识模型,同时考虑和不考虑它们的AD。虽然在单个模型中应用AD约束通常提高了外部预测准确性(以减少化学空间覆盖为代价),但对共识模型的额外益处有限。结果表明,共识模型优于单个模型,在测试集上实现了19.8%的均方根误差(RMSE),而九个单个模型的平均RMSE为20.9%。在其中几个模型中一致识别出的异常值表明存在潜在的实验假象和/或活性悬崖,需要进一步研究。子结构重要性分析表明,模型优先考虑不同的化学特征,而共识平均协调了这些不同的观点。这些发现突出了共识建模在提高预测性能和解决模型局限性方面的价值。未来的工作应集中在扩大化学空间覆盖范围和完善实验数据集,以支持公共卫生保护。