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基于CLPSO增强的混合核支持向量机预测奥希替尼衍生物的表皮生长因子受体抑制作用

Predicting EGFR Inhibitory Effect of Osimertinib Derivatives by Mixed Kernel SVM Enhanced with CLPSO.

作者信息

Li Shaokang, Dong Wenzhe, Qu Aili

机构信息

College of Computer Science and Technology, Qingdao University, Qingdao 266071, China.

School of Economics, Qingdao University, Qingdao 266071, China.

出版信息

Pharmaceuticals (Basel). 2025 Jul 23;18(8):1092. doi: 10.3390/ph18081092.

Abstract

The resistance mutations EGFR in epidermal growth factor receptor (EGFR) are key factors in the reduced efficacy of Osimertinib. Predicting the inhibitory effects of Osimertinib derivatives against these mutations is crucial for the development of more effective inhibitors. This study aims to predict the inhibitory effects of Osimertinib derivatives against EGFR mutations. Six models were established using heuristic method (HM), random forest (RF), gene expression programming (GEP), gradient boosting decision tree (GBDT), polynomial kernel function support vector machine (SVM), and mixed kernel function SVM (MIX-SVM). The descriptors for these models were selected by the heuristic method or XGBoost. Comprehensive learning particle swarm optimizer was adopted to optimize hyperparameters. Additionally, the internal and external validation were performed by leave-one-out cross-validation (QLOO2), 5-fold cross validation (Q5-fold2) and concordance correlation coefficient (CCC), QF12, and QF22. The properties of novel EGFR inhibitors were explored through molecular docking analysis. The model established by MIX-SVM whose kernel function is a convex combination of three regular kernel functions is best: R2 and RMSE for training set and test set are 0.9445, 0.1659 and 0.9490, 0.1814, respectively; QLOO2, Q5-fold2, CCC, QF12, and QF22 are 0.9107, 0.8621, 0.9835, 0.9689, and 0.9680. Based on these results, the IC values of 162 newly designed compounds were predicted using the HM model, and the top four candidates with the most favorable physicochemical properties were subsequently validated through PEA. The MIX-SVM method will provide useful guidance for the design and screening of novel EGFR inhibitors.

摘要

表皮生长因子受体(EGFR)中的耐药性突变是奥希替尼疗效降低的关键因素。预测奥希替尼衍生物对这些突变的抑制作用对于开发更有效的抑制剂至关重要。本研究旨在预测奥希替尼衍生物对EGFR突变的抑制作用。使用启发式方法(HM)、随机森林(RF)、基因表达式编程(GEP)、梯度提升决策树(GBDT)、多项式核函数支持向量机(SVM)和混合核函数SVM(MIX - SVM)建立了六个模型。这些模型的描述符通过启发式方法或XGBoost进行选择。采用综合学习粒子群优化器对超参数进行优化。此外,通过留一法交叉验证(QLOO2)、5折交叉验证(Q5 - fold2)以及一致性相关系数(CCC)、QF12和QF22进行内部和外部验证。通过分子对接分析探索新型EGFR抑制剂的性质。由内核函数为三个正则核函数凸组合的MIX - SVM建立的模型最佳:训练集和测试集的R2和RMSE分别为0.9445、0.1659和0.9490、0.1814;QLOO2、Q5 - fold2、CCC、QF12和QF22分别为0.9107、0.8621、0.9835 、0.9689和0.9680。基于这些结果,使用HM模型预测了162种新设计化合物的IC值,随后通过PEA对具有最有利物理化学性质的前四名候选物进行了验证。MIX - SVM方法将为新型EGFR抑制剂的设计和筛选提供有用的指导。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af2a/12389524/3fa1b688ac6d/pharmaceuticals-18-01092-g001.jpg

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