用分子指纹预测药物脂溶性,比现有方法更准更快。
OWPCP: A Deep Learning Model to Predict Octanol-Water Partition Coefficient
- 用摩根指纹和MACCS键作为输入,结合深度学习预测logP。
- 测试集MAE达0.247,优于所有已有深度学习模型。
- 无需实验数据,适合早期药物研发快速筛选。
化学化合物的理化性质在制药、环境与分离科学中至关重要,其中辛醇-水分配系数(logP)是衡量亲脂性和亲水性的关键指标,影响药物吸收与膜通透性。根据利宾斯基五规则,logP是化学实体稳定性的重要决定因素,需先进计算方法支持。本文提出深度学习模型OWPCP,以摩根指纹和MACCS键为输入特征,基于26,254种化合物的logP值进行训练,涵盖广泛分子结构及分子量、极性表面积差异。通过Keras Tuner与Hyperband算法优化超参数,模型在测试集上达到MAE=0.247,显著优于现有深度学习模型。值得注意的是,尽管某些高精度模型依赖保留时间实验数据,而OWPCP无需任何实验数据即可高效预测logP,尤其在含脂肪族羟基的化合物上表现优异。跨功能团验证显示其预测高度可靠,适用于早期药物发现阶段。
原文摘要 · Abstract (English)
The physicochemical properties of chemical compounds have great importance in several areas, including pharmaceuticals, environmental and separation science. Among these are physicochemical properties such as the octanol-water partition coefficient, which has been considered an important index pointing out lipophilicity and hydrophilicity. It affects drug absorption and membrane permeability. Following Lipinski's rule of five, logP was identified as one of the key determinants of the stability of chemical entities and, as such, needed state-of-the-art methods for measuring lipophilicity. This paper presents a deep-learning model, OWPCP, developed to compute logP using Morgan fingerprints and MACCS keys as input features. It uses the interconnection of such molecular representations with logP values extracted from 26,254 compounds. The dataset was prepared to contain a wide range of chemical structures with differing molecular weights and polar surface area. Hyperparameter optimization was conducted using the Keras Tuner alongside the Hyperband algorithm to enhance the performance. OWPCP demonstrated outstanding performance compared to current computational methods, achieving an MAE=0.247 on the test set and outperforming all previous DL models. Remarkably, while one of the most accurate recent models is based on experimental data on retention time to make predictions, OWPCP manages computing logP efficiently without depending on these factors, being, therefore, very useful during early-stage drug discovery. Our model outperforms the best model, which leverages Retention Time, and our model does not require any experimental data. Further validation of the model performance was done across different functional groups, and it showed very high accuracy, especially for compounds that contain aliphatic OH groups. The results have indicated that OWPCP provides a reliable prediction of logP.
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