MTF-hERG: a Multi-type Features Fusion-based Framework for Predicting hERG Cardiotoxicity of Compounds

The human ether-a-go-go-related gene (hERG) cardiac toxicity of a compound refers to its inhibitory effect on the hERG potassium channel. The hERG channel is crucial for cardiac depolarization, and its blockage can lead to prolongation of the QT interval, triggering arrhythmias and posing life-threatening risks. Therefore, assessing hERG cardiac toxicity is a vital consideration in drug development. Traditional assessment methods are complex and have low throughput, making the development of deep learning models to predict this toxicity essential for enhancing drug development efficiency, reducing risks, and promoting personalized treatment. In this paper, we propose a novel multi-type feature fusion framework, MTF-hERG, for accurately predicting the cardiac toxicity of hERG compounds. This framework integrates various molecular features such as molecular fingerprints, 2D molecular images, and 3D molecular graphs to comprehensively capture the intrinsic structures and properties of compounds. By utilizing fully connected neural networks, DenseNet, and Equivariant Graph Neural Networks for feature extraction, we ensure that the model can precisely identify molecular characteristics associated with hERG blocking activity. Through deep fusion of extracted features and the construction of fully connected layers with different activation functions, we achieve classification predictions of whether a compound is an hERG blocker and regression predictions of its hERG inhibitory capacity. When comparing MTF-hERG with other state-of-the-art methods using benchmark datasets, we found that the average ACC, AUC, AUPR, RMSE, and R² values of MTF-hERG were 0.926, 0.943, 0.913, 0.453, and 0.681, respectively. The results demonstrate that MTF-hERG exhibits excellent predictive performance in various scenarios, significantly outperforming the existing baseline models. Furthermore, the visualization results of MTF-hERG not only reveal the key features and decision mechanisms of the model but also provide valuable support for further optimization of molecular structures. Therefore, the MTF-hERG framework is poised to become a powerful tool for predicting the hERG cardiac toxicity of compounds, offering robust support for drug development and exerting a profound impact on human health.